Exams by July 31; next semester from August 1

The State’s IMR has been on the decreasing trend.

The Regional Science Centre & Planetarium, Kozhikode, is organising “Online Summer Hobby Camp 2020” for students of Classes 7 to 10 from May 18. T

According to the State govt., 29 new cases were reported from Ganjam district followed by Balasore and Angul with 15 and 13 cases.

A fabrication method comprising near-field holography (NFH) with an electron beam lithography (EBL)-written phase mask was developed to fabricate soft X-ray varied-line-spacing gratings (VLSGs). An EBL-written phase mask with an area of 52 mm × 30 mm and a central line density greater than 3000 lines mm−1 was used. The introduction of the EBL-written phase mask substantially simplified the NFH optics for pattern transfer. The characterization of the groove density distribution and diffraction efficiency of the fabricated VLSGs indicates that the EBL–NFH method is feasible and promising for achieving high-accuracy groove density distributions with corresponding image properties. Vertical stray light is suppressed in the soft X-ray spectral range.

The time evolution of the electron density and the resulting time dependence of the X-ray polarizability of a crystal irradiated by highly intense XFEL femtosecond pulses is investigated theoretically. Rate equations for bound electrons and the Boltzmann equation for the unbound electron gas are used in calculations.

Rietveld/MEM analysis applied to synchrotron powder X-ray diffraction data of dehydrated CHA zeolites with catalytically active Cu2+ reveals Cu2+ in both the six- and eight-membered rings in the CHA framework, providing the first complete structural model that accounts for all Cu2+. Density functional theory calculations are used to corroborate the experimental structure and to discuss the Cu2+ coordination in terms of the Al distribution in the framework.

Leading scientists set out resource challenge of meeting net zero emissions in the UK by 2050  The Natural History Museum

The day Folkestone was rocked by one of Kent's worst ever earthquakes  Kent Live

151 homes for Keyworth recommended for approval by council  West Bridgford Wire

Two earthquakes felt by residents in Lochaber  Press and Journal

What is a sinkhole and are they caused by bad weather?  expressandstar.com

'Surrey swarm' quakes 'not caused by oil extraction'  BBC News

Tsunami warning: Britain could be hit by 30m wave - Professor warns of hazards to Britain  Express.co.uk

Scottish Highlands hit by earthquake with magnitude measuring 2.3  The Scottish Sun

'Surrey swarm' earthquakes not caused by nearby oil extraction, study suggests  Science Daily

West Cornwall hit by 2.2 magnitude earthquake | West Country - ITV News  ITV News

Residents speak of shock after being woken by EARTHQUAKE in early hours of morning  Hartlepool Mail

Snowdonia earthquake confirmed by British Geological Survey  Daily Post

Somerset earthquake: Homes shaken by 3.2 magnitude tremor  BBC News

UK sees notable reduction in seismic noise caused by human activity – experts  Aberdeen Evening Express

The syntheses and crystal structures of five 2-benzyl­idene-1-benzosuberone [1-benzosuberone is 6,7,8,9-tetra­hydro-5H-benzo[7]annulen-5-one] derivatives, viz. 2-(4-meth­oxy­benzyl­idene)-1-benzosuberone, C19H18O2, (I), 2-(4-eth­oxy­benzyl­idene)-1-benzosuberone, C20H20O2, (II), 2-(4-benzyl­benzyl­idene)-1-benzosuberone, C25H22O2, (III), 2-(4-chloro­benzyl­idene)-1-benzosuberone, C18H15ClO, (IV) and 2-(4-cyano­benzyl­idene)-1-benzosuberone, C19H15NO, (V), are described. The conformations of the benzosuberone fused six- plus seven-membered ring fragments are very similar in each case, but the dihedral angles between the fused benzene ring and the pendant benzene ring differ somewhat, with values of 23.79 (3) for (I), 24.60 (4) for (II), 33.72 (4) for (III), 29.93 (8) for (IV) and 21.81 (7)° for (V). Key features of the packing include pairwise C—H⋯O hydrogen bonds for (II) and (IV), and pairwise C—H⋯N hydrogen bonds for (V), which generate inversion dimers in each case. The packing for (I) and (III) feature C—H⋯O hydrogen bonds, which lead to [010] and [100] chains, respectively. Weak C—H⋯π inter­actions consolidate the structures and weak aromatic π–π stacking is seen in (II) [centroid–centroid separation = 3.8414 (7) Å] and (III) [3.9475 (7) Å]. A polymorph of (I) crystallized from a different solvent has been reported previously [Dimmock et al. (1999) J. Med. Chem. 42, 1358–1366] in the same space group but with a packing motif based on inversion dimers resembling that seen in (IV) in the present study. The Hirshfeld surfaces and fingerprint plots for (I) and its polymorph are com­pared and structural features of the 2-benzyl­idene-1-benzosuberone family of phases are surveyed.

Highly Brønsted-acidic boron trifluoride monohydrate, a widely used `super acid-catalyst', is a colourless fuming liquid that releases BF3 at room temperature. Com­pared to the liquid com­ponents, i.e. boron trifluoride monohydrate and 1,4-dioxane, their 1:1 adduct, BF3H2O·C4H8O2, is a solid with pronounced thermal stability (m.p. 401–403 K). The crystal structure of the long-time-stable easy-to-handle and weighable com­pound is reported along with new preparative aspects and the results of 1H, 11B, 13C and 19F spectroscopic investigations, particularly documenting its high Brønsted acidity in aceto­nitrile solution. The remarkable stability of solid BF3H2O·C4H8O2 is attributed to the chain structure established by O—H⋯O hydrogen bonds of exceptional strength {O2⋯H1—O1 [O⋯O = 2.534 (3) Å] and O1—H1⋯O3i [2.539 (3) Å] in the concatenating unit >O2⋯H1—O1—H2⋯O3i<}, taking into account the mol­ecular (non-ionic) character of the structural moieties. Indirectly, this structural feature documents the outstanding acidification of the H2O mol­ecule bound to BF3 and reflects the super acid nature of BF3H2O. In detail, the C22(7) zigzag chain system of hydrogen bonding in the title structure is characterized by the double hydrogen-bond donor and double (κO,κO') hydrogen-bond acceptor functionality of the aqua ligand and dioxane molecule, respectively, the almost equal strength of both hydrogen bonds, the approximatety linear arrangement of the dioxane O atoms and the two neighbouring water O atoms. Furthermore, the approximately planar arrangement of B, F and O atoms in sheets perpendicular to the c axis of the ortho­rhom­bic unit cell is a characteristic structural feature.

After crystallization during ionothermal syntheses in phospho­nium-containing ionic liquids, the structure of (NH4)3Al2(PO4)3 [tri­ammonium dialuminum tris­(phosphate)] was refined on the basis of powder X-ray diffraction data from a synchrotron source. (NH4)3Al2(PO4)3 is a member of the structural family with formula A3Al2(PO4)3, where A is a group 1 element, and of which the NH4, K, and Rb forms were previously known. The NH4 form is isostructural with the K form, and was previously solved from single-crystal X-ray data when the material (SIZ-2) crystallized from a choline-containing eutectic mixture [Cooper et al. (2004). Nature, 430, 1012–1017]. Our independent refinement incorporates NH4 groups and shows that these NH4 groups are hydrogen bonded to framework O atoms present in rings containing 12 T sites in a channel along the c-axis direction. We describe structural details of (NH4)3Al2(PO4)3 and discuss differences with respect to isostructural forms.

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.

The asymmetric units of the title compounds, namely, catena-poly[[(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4N1,N4,N8,N11)nickel(II)]-μ-1,3-bis­(3-carboxyl­ato­prop­yl)tetra­methyl­disiloxane-κ2O:O'], [Ni(C10H24O5Si2)(C12H24N4)]n (I), and catena-poly[[[(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4N1,N4,N8,N11)nickel(II)]-μ-4-({[(3-carb­oxy­prop­yl)di­methyl­sil­yl]­oxy}di­methyl­sil­yl)butano­ato-κ2O:O'] per­chlorate], {[Ni(C10H25O5Si2)(C12H24N4)]ClO4}n (II), consist of one (in I) or two crystallographically non-equivalent (in II) centrosymmetric macrocyclic cations and one centrosymmetric dianion (in I) or two centrosymmetric monoanions (in II). In each compound, the metal ion is coordinated by the four secondary N atoms of the macrocyclic ligand, which adopts the most energetically stable trans-III conformation, and the mutually trans O atoms of the carboxyl­ate in a slightly tetra­gonally distorted trans-NiN4O2 octa­hedral coordination geometry. The crystals of both types of compounds are composed of parallel polymeric chains of the macrocyclic cations linked by the anions of the acid running along the [101] and [110] directions in I and II, respectively. In I, each polymeric chain is linked to four neighbouring ones by hydrogen bonding between the NH groups of the macrocycle and the carboxyl­ate O atoms, thus forming a three-dimensional supra­molecular network. In II, each polymeric chain contacts with only two neighbours, forming hydrogen bonds between the partially protonated carb­oxy­lic groups of the bridging ligand. As a result, a lamellar structure is formed with the layers oriented parallel to the (1overline{1}1) plane.

N-[(Z)-2-(2H-1,3,2-Benzodioxaborol-2-yl)-2-phenyl­ethen­yl]-N-(propan-2-yl)aniline, C23H22BNO2, contains a C=C bond that is conjugated with a donor and an acceptor group. An analysis that included similar push–pull olefins revealed that bond lengths in their B—C=C—N core units correlate with the perceived acceptor and donor strength of the groups. The two phenyl groups in the mol­ecule are rotated with respect to the plane that contains the BCCN atoms, and are close enough for significant π-stacking. Definite characterization of the title compound demonstrates, for the first time in a reliable way, that hydro­boration of ynamines with borandiol esters is feasible. Compared to olefin hydro­boration with borane, the ynamine substrate is activated enough to undergo reaction with the less active hydro­boration reagent catecholborane.

Exact and approximate mathematical formulas of equatorial aberration for powder diffraction data collected with an Si strip X-ray detector in continuous-scan integration mode are presented. An approximate formula is applied to treat the experimental data measured with a commercial powder diffractometer.

A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV–visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15–40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.

Copper-containing nitrite reductases (CuNiRs) that convert NO2− to NO via a CuCAT–His–Cys–CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD−, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2− a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclo­butane product. The cyclo­butane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclo­butane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.

Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54–Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine–glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.

3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order β < α < γ. The least stable β polymorph forms within the first 3 min, but this begins to yield the α-form after only 1 min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20 s on crystals of thickness ∼100 nm. Even though the γ-form is thermodynamically the most stable polymorph, kinetics favour the α-form, which dominates after prolonged standing. In the same sample, some β and one crystallite of the γ polymorph were also observed.

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.

Icosahedral quasicrystals (i-phases) in the Al–Cu–Fe system are of great interest because of their perfect quasicrystalline structure and natural occurrences in the Khatyrka meteorite. The natural quasicrystal of composition Al62Cu31Fe7, referred to as i-phase II, is unique because it deviates significantly from the stability field of i-phase and has not been synthesized in a laboratory setting to date. Synthetic i-phases formed in shock-recovery experiments present a novel strategy for exploring the stability of new quasicrystal compositions and prove the impact origin of natural quasicrystals. In this study, an Al–Cu–W graded density impactor (GDI, originally manufactured as a ramp-generating impactor but here used as a target) disk was shocked to sample a full range of Al/Cu starting ratios in an Fe-bearing 304 stainless-steel target chamber. In a strongly deformed region of the recovered sample, reactions between the GDI and the steel produced an assemblage of co-existing Al61.5Cu30.3Fe6.8Cr1.4 i-phase II + stolperite (β, AlCu) + khatyrkite (θ, Al2Cu), an exact match to the natural i-phase II assemblage in the meteorite. In a second experiment, the continuous interface between the GDI and steel formed another more Fe-rich quinary i-phase (Al68.6Fe14.5Cu11.2Cr4Ni1.8), together with stolperite and hollisterite (λ, Al13Fe4), which is the expected assemblage at phase equilibrium. This study is the first laboratory reproduction of i-phase II with its natural assemblage. It suggests that the field of thermodynamically stable icosahedrite (Al63Cu24Fe13) could separate into two disconnected fields under shock pressure above 20 GPa, leading to the co-existence of Fe-rich and Fe-poor i-phases like the case in Khatyrka. In light of this, shock-recovery experiments do indeed offer an efficient method of constraining the impact conditions recorded by quasicrystal-bearing meteorite, and exploring formation conditions and mechanisms leading to quasicrystals.

A large amount of hydrogen circulates inside the Earth, which affects the long-term evolution of the planet. The majority of this hydrogen is stored in deep Earth within the crystal structures of dense minerals that are thermodynamically stable at high pressures and temperatures. To understand the reason for their stability under such extreme conditions, the chemical bonding geometry and cation exchange mechanism for including hydrogen were analyzed in a representative structure of such minerals (i.e. phase E of dense hydrous magnesium silicate) by using time-of-flight single-crystal neutron Laue diffraction. Phase E has a layered structure belonging to the space group R3m and a very large hydrogen capacity (up to 18% H2O weight fraction). It is stable at pressures of 13–18 GPa and temperatures of up to at least 1573 K. Deuterated high-quality crystals with the chemical formula Mg2.28Si1.32D2.15O6 were synthesized under the relevant high-pressure and high-temperature conditions. The nuclear density distribution obtained by neutron diffraction indicated that the O—D dipoles were directed towards neighboring O2− ions to form strong interlayer hydrogen bonds. This bonding plays a crucial role in stabilizing hydrogen within the mineral structure under such high-pressure and high-temperature conditions. It is considered that cation exchange occurs among Mg2+, D+ and Si4+ within this structure, making the hydrogen capacity flexible.

This study made use of a recently developed combination of advanced methods to reveal the atomic structure of a disordered nanocrystalline zeolite using exit wave reconstruction, automated diffraction tomography, disorder modelling and diffraction pattern simulation. By applying these methods, it was possible to determine the so far unknown structures of the hydrous layer silicate RUB-6 and the related zeolite-like material RUB-5. The structures of RUB-5 and RUB-6 contain the same dense layer-like building units (LLBUs). In the case of RUB-5, these building units are interconnected via additional SiO4/2 tetrahedra, giving rise to a framework structure with a 2D pore system consisting of intersecting 8-ring channels. In contrast, RUB-6 contains these LLBUs as separate silicate layers terminated by silanol/sil­oxy groups. Both RUB-6 and RUB-5 show stacking disorder with intergrowths of different polymorphs. The unique structure of RUB-6, together with the possibility for an interlayer expansion reaction to form RUB-5, make it a promising candidate for interlayer expansion with various metal sources to include catalytically active reaction centres.

Current software tools for the automated building of models for macro­molecular X-ray crystal structures are capable of assembling high-quality models for ordered macromolecule and small-molecule scattering components with minimal or no user supervision. Many of these tools also incorporate robust functionality for modelling the ordered water molecules that are found in nearly all macromolecular crystal structures. However, no current tools focus on differentiating these ubiquitous water molecules from other frequently occurring multi-atom solvent species, such as sulfate, or the automated building of models for such species. PeakProbe has been developed specifically to address the need for such a tool. PeakProbe predicts likely solvent models for a given point (termed a `peak') in a structure based on analysis (`probing') of its local electron density and chemical environment. PeakProbe maps a total of 19 resolution-dependent features associated with electron density and two associated with the local chemical environment to a two-dimensional score space that is independent of resolution. Peaks are classified based on the relative frequencies with which four different classes of solvent (including water) are observed within a given region of this score space as determined by large-scale sampling of solvent models in the Protein Data Bank. Designed to classify peaks generated from difference density maxima, PeakProbe also incorporates functionality for identifying peaks associated with model errors or clusters of peaks likely to correspond to multi-atom solvent, and for the validation of existing solvent models using solvent-omit electron-density maps. When tasked with classifying peaks into one of four distinct solvent classes, PeakProbe achieves greater than 99% accuracy for both peaks derived directly from the atomic coordinates of existing solvent models and those based on difference density maxima. While the program is still under development, a fully functional version is publicly available. PeakProbe makes extensive use of cctbx libraries, and requires a PHENIX licence and an up-to-date phenix.python environment for execution.

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.

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallo­graphy beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard–Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.

Noncrystallographic symmetry (NCS) averaging following molecular-replacement phasing is generally the major technique used to solve a structure with several molecules in one asymmetric unit, such as a spherical icosahedral viral particle. As an alternative method to NCS averaging, a new approach to optimize or to refine the electron density directly under NCS constraints is proposed. This method has the same effect as the conventional NCS-averaging method but does not include the process of Fourier synthesis to generate the electron density from amplitudes and the corresponding phases. It has great merit for the solution of structures with limited data that are either twinned or incomplete at low resolution. This method was applied to the case of the T = 1 shell-domain subviral particle of Penaeus vannamei nodavirus with data affected by twinning using the REFMAC5 refinement software.

The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10−4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10−3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.