com (N,N-Diallyldithiocarbamato-κ2S,S')triphenyltin(IV) and bis(N,N-diallyldithiocarbamato-κ2S,S')diphenyltin(IV): crystal structure, Hirshfeld surface analysis and computational study By scripts.iucr.org Published On :: 2020-01-10 The crystal and molecular structures of the title organotin dithiocarbamate compounds, [Sn(C6H5)3(C7H10NS2)] (I) and [Sn(C6H5)2(C7H10NS2)2] (II), present very distinct tin atom coordination geometries. In (I), the dithiocarbamate ligand is asymmetrically coordinating with the resulting C3S2 donor set defining a coordination geometry intermediate between square-pyramidal and trigonal–bipyramidal. In (II), two independent molecules comprise the asymmetric unit, which differ in the conformations of the allyl substituents and in the relative orientations of the tin-bound phenyl rings. The dithiocarbamate ligands in (II) coordinate in an asymmetric mode but the Sn—S bonds are more symmetric than observed in (I). The resulting C2S4 donor set approximates an octahedral coordination geometry with a cis-disposition of the ipso-carbon atoms and with the more tightly bound sulfur atoms approximately trans. The only directional intermolecular contacts in the crystals of (I) and (II) are of the type phenyl-C—H⋯π(phenyl) and vinylidene-C—H⋯π(phenyl), respectively, with each leading to a supramolecular chain propagating along the a-axis direction. The calculated Hirshfeld surfaces emphasize the importance of H⋯H contacts in the crystal of (I), i.e. contributing 62.2% to the overall surface. The only other two significant contacts also involve hydrogen, i.e. C⋯H/H⋯C (28.4%) and S⋯H/H⋯S (8.6%). Similar observations pertain to the individual molecules of (II), which are clearly distinguishable in their surface contacts, with H⋯H being clearly dominant (59.9 and 64.9%, respectively) along with C⋯H/H⋯C (24.3 and 20.1%) and S⋯H/H⋯S (14.4 and 13.6%) contacts. The calculations of energies of interaction suggest dispersive forces make a significant contribution to the stabilization of the crystals. The exception is for the C—H⋯π contacts in (II) where, in addition to the dispersive contribution, significant contributions are made by the electrostatic forces. Full Article text
com The first coordination compound of deprotonated 2-bromonicotinic acid: crystal structure of a dinuclear paddle-wheel copper(II) complex By scripts.iucr.org Published On :: 2020-01-17 A copper(II) dimer with the deprotonated anion of 2-bromonicotinic acid (2-BrnicH), namely, tetrakis(μ-2-bromonicotinato-κ2O:O')bis[aquacopper(II)](Cu—Cu), [Cu2(H2O)2(C6H3BrNO2)4] or [Cu2(H2O)2(2-Brnic)4], (1), was prepared by the reaction of copper(II) chloride dihydrate and 2-bromonicotinic acid in water. The copper(II) ion in 1 has a distorted square-pyramidal coordination environment, achieved by four carboxylate O atoms in the basal plane and the water molecule in the apical position. The pair of symmetry-related copper(II) ions are connected into a centrosymmetric paddle-wheel dinuclear cluster [Cu⋯Cu = 2.6470 (11) Å] via four O,O'-bridging 2-bromonicotinate ligands in the syn-syn coordination mode. In the extended structure of 1, the cluster molecules are assembled into an infinite two-dimensional hydrogen-bonded network lying parallel to the (001) plane via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of various hydrogen-bond ring motifs: dimeric R22(8) and R22(16) loops and a tetrameric R44(16) loop. The Hirshfeld surface analysis was also performed in order to better illustrate the nature and abundance of the intermolecular contacts in the structure of 1. Full Article text
com Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis(pyridin-4-ylmethyl)ethanediamide and 4-chlorobenzoic acid By scripts.iucr.org Published On :: 2020-01-21 The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half molecules of oxalamide (4LH2), as each is disposed about a centre of inversion, and two molecules of 4-chlorobenzoic acid (CBA), each in general positions. Each 4LH2 molecule has a (+)antiperiplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4LH2 molecules. The anti conformation of the carbonyl groups enables the formation of intramolecular amide-N—H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA molecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-molecule aggregates are formed via carboxylic acid-O—H⋯N(pyridyl) hydrogen bonding. These are connected into a supramolecular tape propagating parallel to [100] through amide-N—H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methylene-C—H⋯O(carbonyl) and CBA-C—H⋯O(amide) interactions. As revealed by a more detailed analysis of the molecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O interactions which provide interaction energies approximately one-quarter of those provided by the amide-N—H⋯O(amide) hydrogen bonding sustaining the supramolecular tape. Full Article text
com Crystal structure of a nickel compound comprising two nickel(II) complexes with different ligand environments: [Ni(tren)(H2O)2][Ni(H2O)6](SO4)2 By scripts.iucr.org Published On :: 2020-02-06 The title compound, diaqua[tris(2-aminoethyl)amine]nickel(II) hexaaquanickel(II) bis(sulfate), [Ni(C6H18N4)(H2O)2][Ni(H2O)6](SO4)2 or [Ni(tren)(H2O)2][Ni(H2O)6](SO4)2, consists of two octahedral nickel complexes within the same unit cell. These metal complexes are formed from the reaction of [Ni(H2O)6](SO4) and the ligand tris(2-aminoethyl)amine (tren). The crystals of the title compound are purple, different from those of the starting complex [Ni(H2O)6](SO4), which are turquoise. The reaction was performed both in a 1:1 and 1:2 metal–ligand molar ratio, always yielding the co-precipitation of the two types of crystals. The asymmetric unit of the title compound, which crystallizes in the space group Pnma, consists of two half NiII complexes and a sulfate counter-anion. The mononuclear cationic complex [Ni(tren)(H2O)2]2+ comprises an Ni ion, the tren ligand and two water molecules, while the mononuclear complex [Ni(H2O)6]2+ consists of another Ni ion surrounded by six coordinated water molecules. The [Ni(tren)(H2O)2] and [Ni(H2O)6] subunits are connected to the SO42− counter-anions through hydrogen bonding, thus consolidating the crystal structure. Full Article text
com The crystal structures and Hirshfeld surface analyses of a cadmium(II) and a zinc(II) mononuclear complex of the new tetrakis-substituted pyrazine ligand N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis By scripts.iucr.org Published On :: 2020-02-18 The whole molecule of the cadmium(II) complex, diiodido{N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3N2,N1,N6}cadmium(II), [CdI2(C36H40N6)], (I), of the ligand N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline) (L), is generated by a twofold rotation symmetry; the twofold axis bisects the cadmium atom and the nitrogen atoms of the pyrazine ring. The ligand coordinates in a mono-tridentate manner and the cadmium atom has a fivefold CdN3I2 coordination environment with a distorted shape. In the zinc(II) complex, dichlorido{N,N',N'',N'''-[pyrazine-2,3,5,6-tetrayltetrakis(methylene)]tetrakis(N-methylaniline)-κ3N2,N1,N6}zinc(II) dichloromethane 0.6-solvate, [ZnCl2(C36H40N6)]·0.6CH2Cl2, (II), ligand L also coordinates in a mono-tridentate manner and the zinc atom has a fivefold ZnN3Cl2 coordination environment with a distorted shape. It crystallized as a partial dichloromethane solvate. In the crystal of I, the complex molecules are linked by weak C—H⋯I contacts, forming ribbons propagating along [100]. In the crystal of II, the complex molecules are linked by a series of C—H⋯π interactions, forming layers lying parallel to the (1overline{1}1) plane. In the crystals of both compounds there are metal–halide⋯π(pyrazine) contacts present. The Hirshfeld analyses confirm the importance of the C—H⋯halide contacts in the crystal packing of both compounds. Full Article text
com Crystal structures and comparisons of huntite aluminum borates REAl3(BO3)4 (RE = Tb, Dy and Ho) By scripts.iucr.org Published On :: 2020-02-14 Three huntite-type aluminoborates of stoichiometry REAl3(BO3)4 (RE = Tb, Dy and Ho), namely, terbium/dysprosium/holmium trialuminium tetrakis(borate), were synthesized by slow cooling within a K2Mo3O10 flux with spontaneous crystallization. The crystal structures were determined using single-crystal X-ray diffraction (SC-XRD) data. The synthesized borates are isostructural to the huntite [CaMg3(CO3)4] structure and crystallized within the trigonal R32 space group. The structural parameters were compared to literature data of other huntite REAl3(BO3)4 crystals within the R32 space group. All three borates fit well into the trends calculated from the literature data. The unit-cell parameters and volumes increase linearly with larger RE cations whereas the densities decrease. All of the crystals studied were refined as inversion twins. Full Article text
com Phosphorescent mono- and diiridium(III) complexes cyclometalated by fluorenyl- or phenyl-pyridino ligands with bulky substituents, as prospective OLED dopants By scripts.iucr.org Published On :: 2020-02-18 The crystal structures of tris[9,9-dihexyl-2-(5-methoxypyridin-2-yl-κN)-9H-fluoren-3-yl-κC3]iridium pentane monosolvate, [Ir(C31H38NO)3]·C5H12, (I), di-μ2-chlorido-bis{bis[2-(5-fluoropyridin-2-yl)-9,9-dihexyl-9H-fluoren-3-yl]iridium} pentane 0.3-solvate, [Ir2(C30H35FN)4Cl2]·0.3C5H12, (II), di-μ2-cyanato-bis{bis[9,9-dihexyl-2-(5-methoxypyridin-2-yl)-9H-fluoren-1-yl]iridium} pentane monosolvate, [Ir2(C31H38NO)4(NCO)2(NCO)2]·C5H12, (III), and {μ-N,N'-bis[3,5-bis(trifluoromethyl)phenyl]oxamidato}bis(bis{2-[4-(2,4,6-trimethylphenyl)pyridin-2-yl]phenyl-κ2C1,N'}iridium)–chlorobenzene–pentane (1/2.3/0.4), [Ir2(C20H19N)4(C18H6F12N2O2)]·2.3C6H5Cl·0.4C5H12, (IV), synthesized in the quest for organic light-emitting devices, were determined. The bis-μ2-chloro and bis-μ2-cyanato complexes have ΔΔ and ΛΛ configurations of the distorted octahedral Ir centres in racemic crystals, whereas the oxamido complex has a centrosymmetric (meso) structure with the ΔΛ configuration. The bridging oxamido moiety has a nearly planar anti geometry. All structures show substantial disorder of both host molecules and solvents of crystallization. Full Article text
com Syntheses and crystal structures of a new pyrazine dicarboxamide ligand, N2,N3-bis(quinolin-8-yl)pyrazine-2,3-dicarboxamide, and of a copper perchlorate binuclear complex By scripts.iucr.org Published On :: 2020-02-14 The title pyrazine dicarboxamide ligand, N2,N3-bis(quinolin-8-yl)pyrazine-2,3-dicarboxamide (H2L1), C24H16N6O2, has a twisted conformation with the outer quinoline groups being inclined to the central pyrazine ring by 9.00 (6) and 78.67 (5)°, and by 79.94 (4)° to each other. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming layers parallel to the (10overline{1}) plane, which are in turn linked by offset π–π interactions [intercentroid distances 3.4779 (9) and 3.6526 (8) Å], forming a supramolecular three-dimensional structure. Reaction of the ligand H2L1 with Cu(ClO4)2 in acetonitrile leads to the formation of the binuclear complex, [μ-(3-{hydroxy[(quinolin-8-yl)imino]methyl}pyrazin-2-yl)[(quinolin-8-yl)imino]methanolato]bis[diacetonitrilecopper(II)] tris(perchlorate) acetonitrile disolvate, [Cu2(C24H15N6O2)(CH3CN)4](ClO4)3·2CH3CN or [Cu2(HL1−)(CH3CN)4](ClO4)3·2CH3CN (I). In the cation of complex I, the ligand coordinates to the copper(II) atoms in a bis-tridentate fashion. A resonance-assisted O—H⋯O hydrogen bond is present in the ligand; the position of this H atom was located in a difference-Fourier map. Both copper(II) atoms are fivefold coordinate, being ligated by three N atoms of the ligand and by the N atoms of two acetonitrile molecules. The first copper atom has a perfect square-pyramidal geometry while the second copper atom has a distorted shape. In the crystal, the cation and perchlorate anions are linked by a number of C—H⋯O hydrogen bonds, forming a supramolecular three-dimensional structure. Full Article text
com A binuclear CuII/CaII thiocyanate complex with a Schiff base ligand derived from o-vanillin and ammonia By scripts.iucr.org Published On :: 2020-02-21 The new heterometallic complex, aqua-1κO-bis(μ2-2-iminomethyl-6-methoxyphenolato-1κ2O1,O6:2κ2O1,N)bis(thiocyanato-1κN)calcium(II)copper(II), [CaCu(C8H8NO2)2(NCS)2(H2O)], has been synthesized using a one-pot reaction of copper powder, calcium oxide, o-vanillin and ammonium thiocyanate in methanol under ambient conditions. The Schiff base ligand (C8H9NO2) is generated in situ from the condensation of o-vanillin and ammonia, which is released from the initial NH4SCN. The title compound consists of a discrete binuclear molecule with a {Cu(μ-O)2Ca} core, in which the Cu⋯Ca distance is 3.4275 (6) Å. The coordination geometries of the four-coordinate copper atom in the [CuN2O2] chromophore and the seven-coordinate calcium atom in the [CaO5N2] chromophore can be described as distorted square planar and pentagonal bipyramidal, respectively. In the crystal, O—H⋯S hydrogen bonds between the coordinating water molecules and thiocyanate groups form a supramolecular chain with a zigzag-shaped calcium skeleton. Full Article text
com Whole-molecule disorder of the Schiff base compound 4-chloro-N-(4-nitrobenzylidene)aniline: crystal structure and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2020-02-18 In the crystal of the title Schiff base compound, C13H9ClN2O2, [CNBA; systematic name: (E)-N-(4-chlorophenyl)-1-(4-nitrophenyl)methanimine], the CNBA molecule shows whole-molecule disorder (occupancy ratio 0.65:0.35), with the disorder components related by a twofold rotation about the shorter axis of the molecule. The aromatic rings are inclined to each other by 39.3 (5)° in the major component and by 35.7 (9)° in the minor component. In the crystal, C—H⋯O hydrogen bonds predominate in linking the major components, while weak C—H⋯Cl interactions predominate in linking the minor components. The result is the formation of corrugated layers lying parallel to the ac plane. The crystal packing was analysed using Hirshfeld surface analysis and compared with related structures. Full Article text
com A redetermination of the crystal structure of the mannitol complex NH4[Mo2O5(C6H11O6)]·H2O: hydrogen-bonding scheme and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2020-03-10 The redetermined structure [for the previous study, see: Godfrey & Waters (1975). Cryst. Struct. Commun. 4, 5–8] of ammonium μ-oxido-μ-[1,5,6-trihydroxyhexane-2,3,4-tris(olato)]bis[dioxidomolybdenum(V)] monohydrate, NH4[Mo2(C6H11O6)O5]·H2O, was obtained from an attempt to prepare a glutamic acid complex from the [Co2Mo10H4O38]6− anion. Subsequent study indicated the complex arose from a substantial impurity of mannitol in the glutamic acid sample used. All hydrogen atoms have been located in the present study and the packing displays N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds. A Hirshfeld surface analysis was also performed. Full Article text
com Crystal structure, Hirshfeld surface analysis and computational study of 2-chloro-N-[4-(methylsulfanyl)phenyl]acetamide By scripts.iucr.org Published On :: 2020-03-31 In the title compound, C9H10ClNOS, the amide functional group –C(=O)NH– adopts a trans conformation with the four atoms nearly coplanar. This conformation promotes the formation of a C(4) hydrogen-bonded chain propagating along the [010] direction. The central part of the molecule, including the six-membered ring, the S and N atoms, is fairly planar (r.m.s. deviation of 0.014). The terminal methyl group and the C(=O)CH2 group are slightly deviating out-of-plane while the terminal Cl atom is almost in-plane. Hirshfeld surface analysis of the title compound suggests that the most significant contacts in the crystal are H⋯H, H⋯Cl/Cl⋯H, H⋯C/C⋯H, H⋯O/O⋯H and H⋯S/S⋯H. π–π interactions between inversion-related molecules also contribute to the crystal packing. DFT calculations have been performed to optimize the structure of the title compound using the CAM-B3LYP functional and the 6–311 G(d,p) basis set. The theoretical absorption spectrum of the title compound was calculated using the TD–DFT method. The analysis of frontier orbitals revealed that the π–π* electronic transition was the major contributor to the absorption peak in the electronic spectrum. Full Article text
com The first coordination compound of 6-fluoronicotinate: the crystal structure of a one-dimensional nickel(II) coordination polymer containing the mixed ligands 6-fluoronicotinate and 4,4'-bipyridine By scripts.iucr.org Published On :: 2020-03-10 A one-dimensional nickel(II) coordination polymer with the mixed ligands 6-fluoronicotinate (6-Fnic) and 4,4'-bipyridine (4,4'-bpy), namely, catena-poly[[diaquabis(6-fluoropyridine-3-carboxylato-κO)nickel(II)]-μ-4,4'-bipyridine-κ2N:N'] trihydrate], {[Ni(6-Fnic)2(4,4'-bpy)(H2O)2]·3H2O}n, (1), was prepared by the reaction of nickel(II) sulfate heptahydrate, 6-fluoronicotinic acid (C6H4FNO2) and 4,4'-bipyridine (C10H8N2) in a mixture of water and ethanol. The nickel(II) ion in 1 is octahedrally coordinated by the O atoms of two water molecules, two O atoms from O-monodentate 6-fluoronicotinate ligands and two N atoms from bridging 4,4'-bipyridine ligands, forming a trans isomer. The bridging 4,4'-bipyridine ligands connect symmetry-related nickel(II) ions into infinite one-dimensional polymeric chains running in the [1overline{1}0] direction. In the extended structure of 1, the polymeric chains and lattice water molecules are connected into a three-dimensional hydrogen-bonded network via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of distinct hydrogen-bond ring motifs: octameric R88(24) and hexameric R86(16) loops. Full Article text
com Cis versus trans arrangement of dithiocarbazate ligands in bis-chelated Ni and Cu complexes By scripts.iucr.org Published On :: 2020-04-21 The structures are described of two bis-chelated metal complexes of nickel(II) and copper(II) with S-n-hexyl 3-(1-phenylethylidene)dithiocarbazate Schiff bases in a cis configuration, namely, bis[S-n-hexyl 3-(1-phenylethylidene)dithiocarbazato-κ2N3,S]nickel(II), [Ni(C15H21N2S2)2], and bis[S-n-hexyl 3-(1-phenylethylidene)dithiocarbazato-κ2N3,S]copper(II), [Cu(C15H21N2S2)2]. In both complexes, the metals have distorted square-planar geometries. A search in the Cambridge Structural Database [Groom et al. (2016). Acta Cryst. B72, 171–179] for bis-chelated nickel(II) and copper(II) complexes with similar Schiff bases retrieved 55 and 36 hits for the two metals, respectively. An analysis of the geometrical parameters of complexes showing cis and trans configurations is reported and the values compared with those for the complexes described in this work. Full Article text
com 2-[(2,4,6-Trimethylbenzene)sulfonyl]phthalazin-1(2H)-one: crystal structure, Hirshfeld surface analysis and computational study By scripts.iucr.org Published On :: 2020-04-21 The X-ray crystal structure of the title phthalazin-1-one derivative, C17H16N2O3S {systematic name: 2-[(2,4,6-trimethylbenzene)sulfonyl]-1,2-dihydrophthalazin-1-one}, features a tetrahedral sulfoxide-S atom, connected to phthalazin-1-one and mesityl residues. The dihedral angle [83.26 (4)°] between the organic substituents is consistent with the molecule having the shape of the letter V. In the crystal, phthalazinone-C6-C—H⋯O(sulfoxide) and π(phthalazinone-N2C4)–π(phthalazinone-C6) stacking [inter-centroid distance = 3.5474 (9) Å] contacts lead to a linear supramolecular tape along the a-axis direction; tapes assemble without directional interactions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of the C—H⋯O and π-stacking interactions but, also H⋯H and C—H⋯C contacts. The calculation of the interaction energies indicate the importance of dispersion terms with the greatest energies calculated for the C—H⋯O and π-stacking interactions. Full Article text
com Crystal structure and DFT computational studies of (E)-2,4-di-tert-butyl-6-{[3-(trifluoromethyl)benzyl]iminomethyl}phenol By scripts.iucr.org Published On :: 2020-04-24 The title compound, C23H28F3NO, is an ortho-hydroxy Schiff base compound, which adopts the enol–imine tautomeric form in the solid state. The molecular structure is not planar and the dihedral angle between the planes of the aromatic rings is 85.52 (10)°. The trifluoromethyl group shows rotational disorder over two sites, with occupancies of 0.798 (6) and 0.202 (6). An intramolecular O—H⋯N hydrogen bonding generates an S(6) ring motif. The crystal structure is consolidated by C—H⋯π interactions. The molecular structure was optimized via density functional theory (DFT) methods with the B3LYP functional and LanL2DZ basis set. The theoretical structure is in good agreement with the experimental data. The frontier orbitals and molecular electrostatic potential map were also examined by DFT computations. Full Article text
com A five-coordinate cobalt bis(dithiolene)–phosphine complex [Co(pdt)2(PTA)] (pdt = phenyldithiolene; PTA = 1,3,5-triaza-7-phosphaadamantane) By scripts.iucr.org Published On :: 2020-04-24 The title compound, bis(1,2-diphenyl-2-sulfanylideneethanethiolato-κ2S,S')(1,3,5-triaza-7-phosphaadamantane-κP)cobalt(II) dichloromethane hemisolvate, [Co(pdt)2(PTA)]·0.5C2H4Cl2 or [Co(C14H10S2)2(C6H12N3P)]·0.5C2H4Cl2, contains two phenyldithiolene (pdt) ligands and a 1,3,5-triaza-7-phosphaadamantane (PTA) ligand bound to cobalt with the solvent 1,2-dichloroethane molecule located on an inversion center. The cobalt core exhibits an approximately square-pyramidal geometry with partially reduced thienyl radical monoanionic ligands. The supramolecular network is consolidated by hydrogen-bonding interactions primarily with nitrogen, sulfur and chlorine atoms, as well as parallel displaced π-stacking of the aryl rings. The UV–vis, IR, and CV data are also consistent with monoanionic dithiolene ligands and an overall CoII oxidation state. Full Article text
com SVAT4: a computer program for visualization and analysis of crystal structures By scripts.iucr.org Published On :: 2020-05-05 SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures, including chemical bonds and magnetic moments. A wide range of functions, e.g. revealing atomic layers and polyhedral clusters, are available for further structural analysis. Atomic sizes, colors, appearance, view directions and view modes (orthographic or perspective views) are adjustable. Customized work for the visualization and analysis can be saved and then reloaded. SVAT4 provides a template to simplify the process of preparation of a new data file. SVAT4 can generate high-quality images for publication and animations for presentations. The usability of SVAT4 is broadened by a software suite for simulation and analysis of electron diffraction patterns. Full Article text
com CrystalCMP: automatic comparison of molecular structures By scripts.iucr.org Published On :: 2020-04-23 This article describes new developments in the CrystalCMP software. In particular, an automatic procedure for comparison of molecular packing is presented. The key components are an automated procedure for fragment selection and the replacement of the angle calculation by root-mean-square deviation of atomic positions. The procedure was tested on a large data set taken from the Cambridge Structural Database (CSD) and the results of all the comparisons were saved as an HTML page, which is freely available on the web. The analysis of the results allowed estimation of the threshold for identification of identical packing and allowed duplicates and entries with potentially incorrect space groups to be found in the CSD. Full Article text
com Optimization of crystallization of biological macromolecules using dialysis combined with temperature control By scripts.iucr.org Published On :: 2020-05-05 A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone – which is the optimal location for slow and ordered crystal expansion – by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant–concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination. Full Article text
com Compressive strain formation in surface-damaged crystals By scripts.iucr.org Published On :: 2020-04-23 The mechanism of formation of residual strain in crystals with a damaged surface has been studied by transmission electron microscopy in GaAs wafers ground with sandpaper. The samples showed a dislocation network located near the sample surface penetrating to a depth of a few micrometres, comparable to the size of abrasive particles used for the treatment, and no other types of defects were observed. A simple model for the formation of a compressive strain induced by the dislocation network in the damaged layer is proposed, in satisfactory agreement with the measured strain. The strain is generated by the formation of dislocation half-loops at the crystal surface, having the same component of the Burgers vectors parallel to the surface of the crystal. This is equivalent to the insertion of extra half-planes from the crystal surface to the depth of the damaged zone. This model can be generalized for other crystal structures. An approximate calculation of the strain generated from the observed dislocation distribution in the sample agrees with the proposed model and permits the conclusion that this mechanism is in general sufficient to explain the observed compressive strain, without the need to consider other types of defects. Full Article text
com Energetics of interactions in the solid state of 2-hydroxy-8-X-quinoline derivatives (X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements By scripts.iucr.org Published On :: 2019-07-15 In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) – together with X-ray wavefunction refinement (XWR) – are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures – the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions. Full Article text
com Cryo-EM structure of Neurospora crassa respiratory complex IV By scripts.iucr.org Published On :: 2019-06-26 In fungi, the mitochondrial respiratory chain complexes (complexes I–IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane protein from Neurospora crassa in lipid nanodiscs as cytochrome c oxidase (complex IV) and its structure was determined at 5.5 Å resolution. The map closely resembles the cryo-EM structure of complex IV from Saccharomyces cerevisiae. Its ten subunits are conserved in S. cerevisiae and Bos taurus, but other transmembrane subunits are missing. The different structure of the Cox5a subunit is typical for fungal complex IV and may affect the interaction with complex III in a respiratory supercomplex. Additional density was found between the matrix domains of the Cox4 and Cox5a subunits that appears to be specific to N. crassa. Full Article text
com Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination By scripts.iucr.org Published On :: 2019-07-12 Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal–organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool. Full Article text
com Competitive formation between 2D and 3D metal-organic frameworks: insights into the selective formation and lamination of a 2D MOF By scripts.iucr.org Published On :: 2019-06-12 The structural dimension of metal–organic frameworks (MOFs) is of great importance in defining their properties and thus applications. In particular, 2D layered MOFs are of considerable interest because of their useful applications, which are facilitated by unique structural features of 2D materials, such as a large number of open active sites and high surface areas. Herein, this work demonstrates a methodology for the selective synthesis of a 2D layered MOF in the presence of the competitive formation of a 3D MOF. The ratio of the reactants, metal ions and organic building blocks used during the reaction is found to be critical for the selective formation of a 2D MOF, and is associated with its chemical composition. In addition, the well defined and uniform micro-sized 2D MOF particles are successfully synthesized in the presence of an ultrasonic dispersion. Moreover, the laminated 2D MOF layers are directly synthesized via a modified bottom-up lamination method, a combination of chemical and physical stimuli, in the presence of surfactant and ultrasonication. Full Article text
com A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples By scripts.iucr.org Published On :: 2019-07-10 The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology. Full Article text
com Charge densities in actinide compounds: strategies for data reduction and model building By scripts.iucr.org Published On :: 2019-08-07 The data quality requirements for charge density studies on actinide compounds are extreme. Important steps in data collection and reduction required to obtain such data are summarized and evaluated. The steps involved in building an augmented Hansen–Coppens multipole model for an actinide pseudo-atom are provided. The number and choice of radial functions, in particular the definition of the core, valence and pseudo-valence terms are discussed. The conclusions in this paper are based on a re-examination and improvement of a previously reported study on [PPh4][UF6]. Topological analysis of the total electron density shows remarkable agreement between experiment and theory; however, there are significant differences in the Laplacian distribution close to the uranium atoms which may be due to the effective core potential employed for the theoretical calculations. Full Article text
com The DRS–AIMP2–EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex By scripts.iucr.org Published On :: 2019-08-24 Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S-transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2GST and EPRSGST, respectively). While AIMP2GST and EPRSGST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2GST via hydrogen bonds between the α7–β9 loop of DRS and the β2–α2 loop of AIMP2GST, where Ser156 of AIMP2GST is essential for the assembly. Structural analyses of DRS–AIMP2GST–EPRSGST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC. Full Article text
com A comparative study of single-particle cryo-EM with liquid-nitrogen and liquid-helium cooling By scripts.iucr.org Published On :: 2019-10-22 Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid-helium cooling, although the use of liquid helium is more challenging than that of liquid nitrogen. To date, the benefits of liquid-nitrogen and liquid-helium cooling for single-particle cryo-EM have not been compared quantitatively. With recent technical and computational advances in cryo-EM image recording and processing, such a comparison now seems timely. This study aims to evaluate the relative merits of liquid-helium cooling in present-day single-particle analysis, taking advantage of direct electron detectors. Two data sets for recombinant mouse heavy-chain apoferritin cooled with liquid-nitrogen or liquid-helium to 85 or 17 K were collected, processed and compared. No improvement in terms of resolution or Coulomb potential map quality was found for liquid-helium cooling. Interestingly, beam-induced motion was found to be significantly higher with liquid-helium cooling, especially within the most valuable first few frames of an exposure, thus counteracting any potential benefit of better cryoprotection that liquid-helium cooling may offer for single-particle cryo-EM. Full Article text
com High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography By scripts.iucr.org Published On :: 2019-10-10 High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX. Full Article text
com Synthesis, structure, magnetic and half-metallic properties of Co2−xRuxMnSi (x = 0, 0.25, 0.5, 0.75, 1) compounds By scripts.iucr.org Published On :: 2020-01-01 A series of Co2−xRuxMnSi (x = 0, 0.25, 0.5, 0.75, 1) Heusler compounds were successfully synthesized. The heat-treatment conditions were crucial to make the materials form a single phase with a Heusler structure. With increasing Ru content, the half-metallic gap, lattice parameters and magnetization are continuously adjustable in a wide range. The Co2−xRuxMnSi (x = 0, 0.25) compounds are rigorous half-metals and show a T3 dependence of resistance at low temperature. The Co2−xRuxMnSi (x = 0.5, 0.75, 1) Heusler compounds are the nearly half-metallic materials and show a semiconductive dependence of resistance at low temperature. The experimental magnetization is consistent with that in theory and follows the Slater–Pauling rule. The Curie temperature is higher than 750 K for all Co2−xRuxMnSi Heusler compounds. Full Article text
com Isomorphism: `molecular similarity to crystal structure similarity' in multicomponent forms of analgesic drugs tolfenamic and mefenamic acid By scripts.iucr.org Published On :: 2020-01-07 The non-steroidal anti-inflammatory drugs mefenamic acid (MFA) and tolfenamic acid (TFA) have a close resemblance in their molecular scaffold, whereby a methyl group in MFA is substituted by a chloro group in TFA. The present study demonstrates the isomorphous nature of these compounds in a series of their multicomponent solids. Furthermore, the unique nature of MFA and TFA has been demonstrated while excavating their alternate solid forms in that, by varying the drug (MFA or TFA) to coformer [4-dimethylaminopyridine (DMAP)] stoichiometric ratio, both drugs have produced three different types of multicomponent crystals, viz. salt (1:1; API to coformer ratio), salt hydrate (1:1:1) and cocrystal salt (2:1). Interestingly, as anticipated from the close similarity of TFA and MFA structures, these multicomponent solids have shown an isomorphous relation. A thorough characterization and structural investigation of the new multicomponent forms of MFA and TFA revealed their similarity in terms of space group and structural packing with isomorphic nature among the pairs. Herein, the experimental results are generalized in a broader perspective for predictably identifying any possible new forms of comparable compounds by mapping their crystal structure landscapes. The utility of such an approach is evident from the identification of polymorph VI of TFA from hetero-seeding with isomorphous MFA form I from acetone–methanol (1:1) solution. That aside, a pseudopolymorph of TFA with dimethylformamide (DMF) was obtained, which also has some structural similarity to that of the solvate MFA:DMF. These new isostructural pairs are discussed in the context of solid form screening using structural landscape similarity. Full Article text
com Extraordinary structural complexity of ilmajokite: a multilevel hierarchical framework structure of natural origin By scripts.iucr.org Published On :: 2020-01-01 The crystal structure of ilmajokite, a rare Na-K-Ba-Ce-titanosilicate from the Khibiny mountains, Kola peninsula, Russia, has been solved using single-crystal X-ray diffraction data. The crystal structure is based on a 3D titanosilicate framework consisting of trigonal prismatic titanosilicate (TPTS) clusters centered by Ce3+ in [9]-coordination. Four adjacent TPTS clusters are linked into four-membered rings within the (010) plane and connected via ribbons parallel to 101. The ribbons are organized into layers parallel to (010) and modulated along the a axis with a modulation wavelength of csinβ = 32.91 Å and an amplitude of ∼b/2 = 13.89 Å. The layers are linked by additional silicate tetrahedra. Na+, K+, Ba2+ and H2O groups occur in the framework cavities and have different occupancies and coordination environments. The crystal structure of ilmajokite can be separated into eight hierarchical levels: atoms, coordination polyhedra, TPTS clusters, rings, ribbons, layers, the framework and the whole structure. The information-based analysis allows estimation of the complexity of the structure as 8.468 bits per atom and 11990.129 bits per cell. According to this analysis, ilmajokite is the third-most complex mineral known to date after ewingite and morrisonite, and is the most complex mineral framework structure, comparable in complexity to paulingite-(Ca) (11 590.532 bits per cell). Full Article text
com Evidence for binary Smc complexes lacking kite subunits in archaea By scripts.iucr.org Published On :: 2020-01-16 SMC complexes play a central role in chromosome organization in all domains of life. The bacterial Smc–ScpAB complex is a three-subunit complex composed of Smc, ScpA and ScpB. ScpA bridges the two ATPase domains of the Smc homodimer, while ScpB, which belongs to the kite family of proteins, interacts with ScpA. The three subunits are known to be equally important for the function of Smc–ScpAB in bacteria. From crystallographic and biochemical studies, evidence is provided that six archaeal ScpA proteins are unable to interact with the only putative ScpB found in these species. Structure-based sequence alignment reveals that these archaeal ScpAs lack the ScpB-binding segment that is commonly present in the middle of bacterial ScpA sequences, which is thus responsible for their inability to interact with ScpB. ScpA proteins lacking the ScpB-binding segment are found to prevail in archaea. Moreover, two archaeal ScpA proteins with a longer middle region also failed to bind their putative ScpB partner. Furthermore, all or most species belonging to five out of 14 euryarchaeotal orders contain Smc and ScpA but not a detectable ScpB homologue. These data support the notion that archaeal Smc-based complexes generally function as a two-subunit complex composed of only Smc and ScpA. Full Article text
com 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow By scripts.iucr.org Published On :: 2020-01-16 Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX. Full Article text
com Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals By scripts.iucr.org Published On :: 2020-02-26 Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme. Full Article text
com Comparing the backfilling of mesoporous titania thin films with hole conductors of different sizes sharing the same mass density By scripts.iucr.org Published On :: 2020-02-12 Efficient infiltration of a mesoporous titania matrix with conducting organic polymers or small molecules is one key challenge to overcome for hybrid photovoltaic devices. A quantitative analysis of the backfilling efficiency with time-of-flight grazing incidence small-angle neutron scattering (ToF-GISANS) and scanning electron microscopy (SEM) measurements is presented. Differences in the morphology due to the backfilling of mesoporous titania thin films are compared for the macromolecule poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5-b']dithiophene-2,6-diyl-alt-(4-(2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene-)-2-carboxylate-2-6-diyl)] (PTB7-Th) and the heavy-element containing small molecule 2-pinacolboronate-3-phenylphenanthro[9,10-b]tellurophene (PhenTe-BPinPh). Hence, a 1.7 times higher backfilling efficiency of almost 70% is achieved for the small molecule PhenTe-BPinPh compared with the polymer PTB7-Th despite sharing the same volumetric mass density. The precise characterization of structural changes due to backfilling reveals that the volumetric density of backfilled materials plays a minor role in obtaining good backfilling efficiencies and interfaces with large surface contact. Full Article text
com Probing the structural pathway of conformational polymorph nucleation by comparing a series of α,ω-alkanedicarboxylic acids By scripts.iucr.org Published On :: 2020-03-26 Herein the nucleation pathway of conformational polymorphs was revealed by studying the relationships and distinctions among a series of α,ω-alkanedicarboxylic acids [HOOC–(CH2)n−2–COOH, named DAn, where n = 5, 7, 9, 11, 13, 15] in the solid state and in solution. Their polymorphic outcomes, with the exception of DA5, show solvent dependence: form I with conformation I crystallizes from solvents with hydrogen-bond donating (HBD) ability, whereas form II with conformation II crystallizes preferentially from solvents with no HBD ability. In contrast, form II of DA5 does not crystallize in any of the solvents used. Quantum mechanical computation showed that there is no direct conformational link between the solvents and the resultant polymorphic outcomes. Surprisingly, solute aggregates were found in no-HBD solvents by Fourier transform infrared spectroscopy, and only monomers could be detected in HBD solvents, suggesting stronger solvation. Furthermore, it was found that all six compounds including DA5 followed the same pattern in solution. Moreover, crystal-packing efficiency calculations and stability tests stated that dimorphs of DA5 bear a greater stability difference than others. These suggest that the rearrangement from conformation II to I could not be limited by hard desolvation in HBD solvents, where form I was also obtained. In other systems, metastable II was produced in the same solvents, probably as a result of the rearrangement being limited by hard desolvation. In this work, a comparative study uncovers the proposed nucleation pathway: difficulty in desolvation has a remarkable effect on the result of rearrangement and nucleation outcome. Full Article text
com A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface By scripts.iucr.org Published On :: 2020-03-28 Human septins 3, 9 and 12 are the only members of a specific subgroup of septins that display several unusual features, including the absence of a C-terminal coiled coil. This particular subgroup (the SEPT3 septins) are present in rod-like octameric protofilaments but are lacking in similar hexameric assemblies, which only contain representatives of the three remaining subgroups. Both hexamers and octamers can self-assemble into mixed filaments by end-to-end association, implying that the SEPT3 septins may facilitate polymerization but not necessarily function. These filaments frequently associate into higher order complexes which associate with biological membranes, triggering a wide range of cellular events. In the present work, a complete compendium of crystal structures for the GTP-binding domains of all of the SEPT3 subgroup members when bound to either GDP or to a GTP analogue is provided. The structures reveal a unique degree of plasticity at one of the filamentous interfaces (dubbed NC). Specifically, structures of the GDP and GTPγS complexes of SEPT9 reveal a squeezing mechanism at the NC interface which would expel a polybasic region from its binding site and render it free to interact with negatively charged membranes. On the other hand, a polyacidic region associated with helix α5', the orientation of which is particular to this subgroup, provides a safe haven for the polybasic region when retracted within the interface. Together, these results suggest a mechanism which couples GTP binding and hydrolysis to membrane association and implies a unique role for the SEPT3 subgroup in this process. These observations can be accounted for by constellations of specific amino-acid residues that are found only in this subgroup and by the absence of the C-terminal coiled coil. Such conclusions can only be reached owing to the completeness of the structural studies presented here. Full Article text
com Structures of substrate- and product-bound forms of a multi-domain copper nitrite reductase shed light on the role of domain tethering in protein complexes By scripts.iucr.org Published On :: 2020-04-25 Copper-containing nitrite reductases (CuNiRs) are found in all three kingdoms of life and play a major role in the denitrification branch of the global nitrogen cycle where nitrate is used in place of dioxygen as an electron acceptor in respiratory energy metabolism. Several C- and N-terminal redox domain tethered CuNiRs have been identified and structurally characterized during the last decade. Our understanding of the role of tethered domains in these new classes of three-domain CuNiRs, where an extra cytochrome or cupredoxin domain is tethered to the catalytic two-domain CuNiRs, has remained limited. This is further compounded by a complete lack of substrate-bound structures for these tethered CuNiRs. There is still no substrate-bound structure for any of the as-isolated wild-type tethered enzymes. Here, structures of nitrite and product-bound states from a nitrite-soaked crystal of the N-terminal cupredoxin-tethered enzyme from the Hyphomicrobium denitrificans strain 1NES1 (Hd1NES1NiR) are provided. These, together with the as-isolated structure of the same species, provide clear evidence for the role of the N-terminal peptide bearing the conserved His27 in water-mediated anchoring of the substrate at the catalytic T2Cu site. Our data indicate a more complex role of tethering than the intuitive advantage for a partner-protein electron-transfer complex by narrowing the conformational search in such a combined system. Full Article text
com Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68 By scripts.iucr.org Published On :: 2019-07-02 Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin. Full Article text
com LAT1 (SLC7A5) and CD98hc (SLC3A2) complex dynamics revealed by single-particle cryo-EM By scripts.iucr.org Published On :: 2019-06-28 Solute carriers are a large class of transporters that play key roles in normal and disease physiology. Among the solute carriers, heteromeric amino-acid transporters (HATs) are unique in their quaternary structure. LAT1–CD98hc, a HAT, transports essential amino acids and drugs across the blood–brain barrier and into cancer cells. It is therefore an important target both biologically and therapeutically. During the course of this work, cryo-EM structures of LAT1–CD98hc in the inward-facing conformation and in either the substrate-bound or apo states were reported to 3.3–3.5 Å resolution [Yan et al. (2019), Nature (London), 568, 127–130]. Here, these structures are analyzed together with our lower resolution cryo-EM structure, and multibody 3D auto-refinement against single-particle cryo-EM data was used to characterize the dynamics of the interaction of CD98hc and LAT1. It is shown that the CD98hc ectodomain and the LAT1 extracellular surface share no substantial interface. This allows the CD98hc ectodomain to have a high degree of movement within the extracellular space. The functional implications of these aspects are discussed together with the structure determination. Full Article text
com Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX By scripts.iucr.org Published On :: 2019-08-22 Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX–inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IXSV; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IXSV for crystallographic studies and their structural comparison are described. Four CA IXSV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal unit-cell packing reveals different crystallographic and noncrystallographic dimers of CA IXSV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IXSV for neutron protein crystallography. Full Article text
com X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein By scripts.iucr.org Published On :: 2019-08-28 The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe–4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer. Full Article text
com Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin By scripts.iucr.org Published On :: 2019-11-19 Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures. Full Article text
com Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum By scripts.iucr.org Published On :: 2020-01-01 Corrections are published for the article by Caldararu et al. [(2019), Acta Cryst. D75, 368–380]. Full Article text
com ALIXE: a phase-combination tool for fragment-based molecular replacement By scripts.iucr.org Published On :: 2020-02-25 Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default. Full Article text
com Radiochromic film dosimetry in synchrotron radiation breast computed tomography: a phantom study By scripts.iucr.org Published On :: 2020-04-22 This study relates to the INFN project SYRMA-3D for in vivo phase-contrast breast computed tomography using the SYRMEP synchrotron radiation beamline at the ELETTRA facility in Trieste, Italy. This peculiar imaging technique uses a novel dosimetric approach with respect to the standard clinical procedure. In this study, optimization of the acquisition procedure was evaluated in terms of dose delivered to the breast. An offline dose monitoring method was also investigated using radiochromic film dosimetry. Various irradiation geometries have been investigated for scanning the prone patient's pendant breast, simulated by a 14 cm-diameter polymethylmethacrylate cylindrical phantom containing pieces of calibrated radiochromic film type XR-QA2. Films were inserted mid-plane in the phantom, as well as wrapped around its external surface, and irradiated at 38 keV, with an air kerma value that would produce an estimated mean glandular dose of 5 mGy for a 14 cm-diameter 50% glandular breast. Axial scans were performed over a full rotation or over 180°. The results point out that a scheme adopting a stepped rotation irradiation represents the best geometry to optimize the dose distribution to the breast. The feasibility of using a piece of calibrated radiochromic film wrapped around a suitable holder around the breast to monitor the scan dose offline is demonstrated. Full Article text
com Versatile compact heater design for in situ nano-tomography by transmission X-ray microscopy By scripts.iucr.org Published On :: 2020-04-16 A versatile, compact heater designed at National Synchrotron Light Source-II for in situ X-ray nano-imaging in a full-field transmission X-ray microscope is presented. Heater design for nano-imaging is challenging, combining tight spatial constraints with stringent design requirements for the temperature range and stability. Finite-element modeling and analytical calculations were used to determine the heater design parameters. Performance tests demonstrated reliable and stable performance, including maintaining the exterior casing close to room temperature while the heater is operating at above 1100°C, a homogenous heating zone and small temperature fluctuations. Two scientific experiments are presented to demonstrate the heater capabilities: (i) in situ 3D nano-tomography including a study of metal dealloying in a liquid molten salt extreme environment, and (ii) a study of pore formation in icosahedral quasicrystals. The progression of structural changes in both studies were clearly resolved in 3D, showing that the new heater enables powerful capabilities to directly visualize and quantify 3D morphological evolution of materials under real conditions by X-ray nano-imaging at elevated temperature during synthesis, fabrication and operation processes. This heater design concept can be applied to other applications where a precise, compact heater design is required. Full Article text
com Linearly polarized X-ray fluorescence computed tomography based on a Thomson scattering light source: a Monte Carlo study By scripts.iucr.org Published On :: 2020-04-06 A Thomson scattering X-ray source can provide quasi-monochromatic, continuously energy-tunable, polarization-controllable and high-brightness X-rays, which makes it an excellent tool for X-ray fluorescence computed tomography (XFCT). In this paper, we examined the suppression of Compton scattering background in XFCT using the linearly polarized X-rays and the implementation feasibility of linearly polarized XFCT based on this type of light source, concerning the influence of phantom attenuation and the sampling strategy, its advantage over K-edge subtraction computed tomography (CT), the imaging time, and the potential pulse pile-up effect by Monte Carlo simulations. A fan beam and pinhole collimator geometry were adopted in the simulation and the phantom was a polymethyl methacrylate cylinder inside which were gadolinium (Gd)-loaded water solutions with Gd concentrations ranging from 0.2 to 4.0 wt%. Compared with the case of vertical polarization, Compton scattering was suppressed by about 1.6 times using horizontal polarization. An accurate image of the Gd-containing phantom was successfully reconstructed with both spatial and quantitative identification, and good linearity between the reconstructed value and the Gd concentration was verified. When the attenuation effect cannot be neglected, one full cycle (360°) sampling and the attenuation correction became necessary. Compared with the results of K-edge subtraction CT, the contrast-to-noise ratio values of XFCT were improved by 2.03 and 1.04 times at low Gd concentrations of 0.2 and 0.5 wt%, respectively. When the flux of a Thomson scattering light source reaches 1013 photons s−1, it is possible to finish the data acquisition of XFCT at the minute or second level without introducing pulse pile-up effects. Full Article text