is BGS announces collaboration with Ordnance Survey - British Geological Survey By news.google.com Published On :: Wed, 29 May 2024 07:00:00 GMT BGS announces collaboration with Ordnance Survey British Geological Survey Full Article
is Geochemistry and health in the Kenyan Rift Valley - British Geological Survey By news.google.com Published On :: Thu, 01 Aug 2024 11:06:32 GMT Geochemistry and health in the Kenyan Rift Valley British Geological Survey Full Article
is Quake it off: Taylor Swift concerts shake Edinburgh - British Geological Survey By news.google.com Published On :: Thu, 13 Jun 2024 07:00:00 GMT Quake it off: Taylor Swift concerts shake Edinburgh British Geological Survey Full Article
is Tris(4-chlorophenyl) phosphate By journals.iucr.org Published On :: In the title compound, the symmetric phosphate derived from para-chlorophenol and phosphoric acid, two of the three aromatic moieties adopt syn-orientation towards the P&z-dbnd;O bond while the last chlorophenol ring is pointing away from this bond. In the extended structure, C—H⋯O bonds connect the individual molecules into sheets lying perpendicular to the crystallographic b axis. Full Article text
is Structural insights into 1,4-bis(neopentyloxy)pillar[5]arene and the pyridine host–guest system By journals.iucr.org Published On :: The crystal structure of a neopentyloxypillar[5]arene with two pyridine molecules encapsulated in the macrocyclic cavity is reported. Full Article text
is A contribution to the crystal chemistry and topology of organic thiosulfates: bis(1-methylpiperazinium)·S2O3·H2O versus 1-methylpiperazinediium·S2O3·3H2O By journals.iucr.org Published On :: Crystal structure and topology of two new thiosulfates formed with mono- and diprotonated species of 1-methylpiperazine is reported. Full Article text
is Synthesis and structural study of the partially disordered complex hexagonal phase δ1-MnZn9.7 By journals.iucr.org Published On :: A detailed structural characterization of the δ1-MnZn9.7 phase is presented. Full Article text
is Atypical phase transition, twinning and ferroelastic domain structure in bis(ethylenediammonium) tetrabromozincate(II) bromide, [NH3(CH2)2NH3]2[ZnBr4]Br2 By journals.iucr.org Published On :: A unique phase transition, twinning and ferroelastic domain structure in [NH3(CH2)2NH3]2[ZnBr4]Br2 is found. The new additional domain structure is observed at the phase transition on heating, which is preserved after cooling to room temperature. Full Article text
is Coordination geometry flexibility driving supramolecular isomerism of Cu/Mo pillared-layer hybrid networks By journals.iucr.org Published On :: The hydrothermal synthesis and structural characterization of four novel 3D pillared-layer metal–organic frameworks are studied, revealing how the malleability of copper coordination geometries drives diverse supramolecular isomerism. The findings provide new insights into designing advanced hybrid materials with tailored properties, emphasizing the significant role of reaction conditions and metal ion flexibility in determining network topologies. Full Article text
is Polymorphism of Pb5(PO4)3OHδ within the LK-99 mixture By journals.iucr.org Published On :: A new orthorhombic crystal Pb5(PO4)3OHδ of space-group symmetry Pnma significantly differs differing from the hexagonal apatite phases of Pb10(PO4)6O and Pb5(PO4)3OH. Full Article text
is Density functional theory investigation of the phase transition, elastic and thermal characteristics for AuMTe2(M = Ga, In) chalcopyrite compounds By journals.iucr.org Published On :: This study presents the first theoretical predictions of the phase transitions, elastic properties, and thermal behavior of AuMTe2 (M = Ga, In) chalcopyrite compounds. Using density functional theory and the quasi-harmonic Debye model, key mechanical and thermodynamic properties are analyzed, offering insights valuable for future experimental validation. Full Article text
is Atypical phase transition, twinning and ferroelastic domain structure in bis(ethylenediammonium) tetrabromozincate(II) bromide, [NH3(CH2)2NH3]2[ZnBr4]Br2 By journals.iucr.org Published On :: 2024-11-04 Single-crystal growth, differential thermal analysis (DTA), derivative thermogravimetry (DTG), differential scanning calorimetry (DSC), X-ray structural studies and polarized microscopy observations of bis(ethylenediammonium) tetrabromozincate(II) bromide [NH3(CH2)2NH3]2[ZnBr4]Br2 are presented. A reversible phase transition is described. At room temperature, the complex crystallizes in the monoclinic system. In some cases, the single crystals are twinned into two or more large domains of ferroelastic type with domain walls in the (100) crystallographic plane. DTA and DTG measurements show chemical stability of the crystal up to ∼538 K. In the DSC studies, a reversible isostructural phase transition was revealed at ∼526/522 K on heating/cooling run, respectively. Optical observation on the heating run reveals that at the phase transition the plane of twinning (domain wall) does not disappear and additionally the appearance of a new domain structure of ferroelastic type with domain walls in the planes (101), (101), (100) and (001) is observed. The domain structure pattern is preserved after cooling to the room-temperature phase and the symmetry of this phase is unchanged. Full Article text
is Synthesis and structural study of the partially disordered complex hexagonal phase δ1-MnZn9.7 By journals.iucr.org Published On :: 2024-10-02 A detailed structural analysis of the Zn-rich δ1-MnZn9.7 phase using single-crystal X-ray diffraction is presented. The δ1 phase has been synthesized by the high-temperature synthetic route. The structure crystallizes in space group P63/mmc (Pearson symbol hP556) with unit-cell parameters: a = b = 12.9051 (2) Å and c = 57.640 (1) Å. The 556 atoms are distributed over 52 Wyckoff positions in the hexagonal unit cell: seven ordered Mn sites, 37 ordered Zn sites and eight positionally disordered Zn sites. The structure predominantly consists of Frank–Kasper polyhedra (endohedral icosahedra Zn12 and icosioctahedron Zn16) and four distinct types of glue Zn atoms. The structure comprises a 127-atom supercluster (Mn13Zn114), a 38-atom extended Pearce cluster (Mn3Zn35), a 46-atom L-tetrahedron (Mn4Zn42), a Friauf polyhedron (Zn17), a disordered icosahedral cluster (MnZn12) and four glue Zn atoms. Positionally disordered Zn sites around an Mn site can be visualized as the superimposition of three differently oriented Zn12 icosahedra. Full Article text
is Assessment of the exchange-hole dipole moment dispersion correction for the energy ranking stage of the seventh crystal structure prediction blind test By journals.iucr.org Published On :: 2024-10-15 The seventh blind test of crystal structure prediction (CSP) methods substantially increased the level of complexity of the target compounds relative to the previous tests organized by the Cambridge Crystallographic Data Centre. In this work, the performance of density-functional methods is assessed using numerical atomic orbitals and the exchange-hole dipole moment dispersion correction (XDM) for the energy-ranking phase of the seventh blind test. Overall, excellent performance was seen for the two rigid molecules (XXVII, XXVIII) and for the organic salt (XXXIII). However, for the agrochemical (XXXI) and pharmaceutical (XXXII) targets, the experimental polymorphs were ranked fairly high in energy amongst the provided candidate structures and inclusion of thermal free-energy corrections from the lattice vibrations was found to be essential for compound XXXI. Based on these results, it is proposed that the importance of vibrational free-energy corrections increases with the number of rotatable bonds. Full Article text
is X-ray crystallographic structure of a novel enantiopure chiral isothiourea with potential applications in enantioselective synthesis By journals.iucr.org Published On :: 2024-01-01 The synthesis of a chiral isothiourea, namely, (4aR,8aR)-3-phenyl-4a,5,6,7,8,8a-hexahydrobenzo[4,5]imidazo[2,1-b]thiazol-9-ium bromide, C15H17N2S+·Br−, with potential organocatalytic and anti-inflammatory activity is reported. The preparation of the heterocycle of interest was carried out in two high-yielding steps. The hydrobromide salt of the isothiourea of interest provided suitable crystals for X-ray diffraction analysis, the results of which are reported. Salient observations from this analysis are the near perpendicular arrangement of the phenyl ring and the mean plane of the heterocycle. This conformational characteristic may be relevant with regard the stereoselectivity induced by the chiral isothiourea in asymmetric reactions. Furthermore, evidence was found for the existence of an S...Br− halogen bond. Full Article text
is Synthesis and crystal structure of Ba2Y0.87(1)Mn1.71(1)Te5 By journals.iucr.org Published On :: 2024-01-01 We report the structural characterization of a new quaternary telluride, Ba2Y0.87(1)Mn1.71(1)Te5, which was synthesized by the direct reaction of the elements inside a vacuum-sealed fused-silica tube. The quaternary phase is the first member of the Ba–M–Mn–Te system (M = Sc and Y). The composition and structure of the phase were elucidated using SEM–EDX (scanning electron microscopy–energy dispersive X-ray spectrometry) and single-crystal X-ray diffraction (SCXRD) studies. The title phase is nonstoichiometric and crystallizes in the monoclinic system (space group C2/m) having the refined unit-cell parameters a = 15.1466 (8), b = 4.5782 (3), c = 10.6060 (7) Å and β = 116.956 (2)°, with two formula units (Z = 2). The pseudo-two-dimensional crystal structure of Ba2Y0.87(1)Mn1.71(1)Te5 consists of distorted YTe6 octahedra and MnTe4 tetrahedra as the building blocks of the structure. The YTe6 octahedra are arranged to form infinite one-dimensional chains by sharing edges along the [010] direction. These chains are further connected to the MnTe4 tetrahedra along the c axis to create layered two-dimensional polyanionic [Y0.87(1)Mn1.71(1)Te5]4− units. The stuffing of Ba2+ cations in between the layers of [Y0.87(1)Mn1.71(1)Te5]4− anions brings the charge neutrality of the structure. Each Ba atom in the structure sits at the centre of a distorted monocapped trigonal prism-like polyhedron of seven Te atoms. Full Article text
is Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning By journals.iucr.org Published On :: 2024-02-29 Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data. Full Article text
is ClusterFinder: a fast tool to find cluster structures from pair distribution function data By journals.iucr.org Published On :: 2024-02-29 A novel automated high-throughput screening approach, ClusterFinder, is reported for finding candidate structures for atomic pair distribution function (PDF) structural refinements. Finding starting models for PDF refinements is notoriously difficult when the PDF originates from nanoclusters or small nanoparticles. The reported ClusterFinder algorithm can screen 104 to 105 candidate structures from structural databases such as the Inorganic Crystal Structure Database (ICSD) in minutes, using the crystal structures as templates in which it looks for atomic clusters that result in a PDF similar to the target measured PDF. The algorithm returns a rank-ordered list of clusters for further assessment by the user. The algorithm has performed well for simulated and measured PDFs of metal–oxido clusters such as Keggin clusters. This is therefore a powerful approach to finding structural cluster candidates in a modelling campaign for PDFs of nanoparticles and nanoclusters. Full Article text
is Permissible domain walls in monoclinic ferroelectrics. Part II. The case of MC phases By journals.iucr.org Published On :: 2024-04-29 Monoclinic ferroelectric phases are prevalent in various functional materials, most notably mixed-ion perovskite oxides. These phases can manifest as regularly ordered long-range crystallographic structures or as macroscopic averages of the self-assembled tetragonal/rhombohedral nanodomains. The structural and physical properties of monoclinic ferroelectric phases play a pivotal role when exploring the interplay between ferroelectricity, ferroelasticity, giant piezoelectricity and multiferroicity in crystals, ceramics and epitaxial thin films. However, the complex nature of this subject presents challenges, particularly in deciphering the microstructures of monoclinic domains. In Paper I [Biran & Gorfman (2024). Acta Cryst. A80, 112–128] the geometrical principles governing the connection of domain microstructures formed by pairing MAB type monoclinic domains were elucidated. Specifically, a catalog was established of `permissible domain walls', where `permissible', as originally introduced by Fousek & Janovec [J. Appl. Phys. (1969), 40, 135–142], denotes a mismatch-free connection between two monoclinic domains along the corresponding domain wall. The present article continues the prior work by elaborating on the formalisms of permissible domain walls to describe domain microstructures formed by pairing the MC type monoclinic domains. Similarly to Paper I, 84 permissible domain walls are presented for MC type domains. Each permissible domain wall is characterized by Miller indices, the transformation matrix between the crystallographic basis vectors of the domains and, crucially, the expected separation of Bragg peaks diffracted from the matched pair of domains. All these parameters are provided in an analytical form for easy and intuitive interpretation of the results. Additionally, 2D illustrations are provided for selected instances of permissible domain walls. The findings can prove valuable for various domain-related calculations, investigations involving X-ray diffraction for domain analysis and the description of domain-related physical properties. Full Article text
is Bond topology of chain, ribbon and tube silicates. Part II. Geometrical analysis of infinite 1D arrangements of (TO4)n− tetrahedra By journals.iucr.org Published On :: 2024-04-29 In Part I of this series, all topologically possible 1-periodic infinite graphs (chain graphs) representing chains of tetrahedra with up to 6–8 vertices (tetrahedra) per repeat unit were generated. This paper examines possible restraints on embedding these chain graphs into Euclidean space such that they are compatible with the metrics of chains of tetrahedra in observed crystal structures. Chain-silicate minerals with T = Si4+ (plus P5+, V5+, As5+, Al3+, Fe3+, B3+, Be2+, Zn2+ and Mg2+) have a grand nearest-neighbour 〈T–T〉 distance of 3.06±0.15 Å and a minimum T⋯T separation of 3.71 Å between non-nearest-neighbour tetrahedra, and in order for embedded chain graphs (called unit-distance graphs) to be possible atomic arrangements in crystals, they must conform to these metrics, a process termed equalization. It is shown that equalization of all acyclic chain graphs is possible in 2D and 3D, and that equalization of most cyclic chain graphs is possible in 3D but not necessarily in 2D. All unique ways in which non-isomorphic vertices may be moved are designated modes of geometric modification. If a mode (m) is applied to an equalized unit-distance graph such that a new geometrically distinct unit-distance graph is produced without changing the lengths of any edges, the mode is designated as valid (mv); if a new geometrically distinct unit-distance graph cannot be produced, the mode is invalid (mi). The parameters mv and mi are used to define ranges of rigidity of the unit-distance graphs, and are related to the edge-to-vertex ratio, e/n, of the parent chain graph. The program GraphT–T was developed to embed any chain graph into Euclidean space subject to the metric restraints on T–T and T⋯T. Embedding a selection of chain graphs with differing e/n ratios shows that the principal reason why many topologically possible chains cannot occur in crystal structures is due to violation of the requirement that T⋯T > 3.71 Å. Such a restraint becomes increasingly restrictive as e/n increases and indicates why chains with stoichiometry TO<2.5 do not occur in crystal structures. Full Article text
is GraphT–T (V1.0Beta), a program for embedding and visualizing periodic graphs in 3D Euclidean space By journals.iucr.org Published On :: 2024-04-29 Following the work of Day & Hawthorne [Acta Cryst. (2022), A78, 212–233] and Day et al. [Acta Cryst. (2024), A80, 258–281], the program GraphT–T has been developed to embed graphical representations of observed and hypothetical chains of (SiO4)4− tetrahedra into 2D and 3D Euclidean space. During embedding, the distance between linked vertices (T–T distances) and the distance between unlinked vertices (T⋯T separations) in the resultant unit-distance graph are restrained to the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is restrained to be equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. The notional interactions between vertices are described by a 3D spring-force algorithm in which the attractive forces between linked vertices behave according to Hooke's law and the repulsive forces between unlinked vertices behave according to Coulomb's law. Embedding parameters (i.e. spring coefficient, k, and Coulomb's constant, K) are iteratively refined during embedding to determine if it is possible to embed a given graph to produce a unit-distance graph with T–T distances and T⋯T separations that are compatible with the observed T–T distances and T⋯T separations in crystal structures. The resultant unit-distance graphs are denoted as compatible and may form crystal structures if and only if all distances between linked vertices (T–T distances) agree with the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. If the unit-distance graph does not satisfy these conditions, it is considered incompatible and the corresponding chain of tetrahedra is unlikely to form crystal structures. Using GraphT–T, Day et al. [Acta Cryst. (2024), A80, 258–281] have shown that several topological properties of chain graphs influence the flexibility (and rigidity) of the corresponding chains of Si tetrahedra and may explain why particular compatible chain arrangements (and the minerals in which they occur) are more common than others and/or why incompatible chain arrangements do not occur in crystals despite being topologically possible. Full Article text
is Instrumental broadening and the radial pair distribution function with 2D detectors By journals.iucr.org Published On :: 2024-07-15 The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB6 from measurements made in different-sized capillaries. Full Article text
is High-resolution double vision of the allosteric phosphatase PTP1B By journals.iucr.org Published On :: 2024-01-01 Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including non-isomorphism. Here, the highest resolution crystal structure of apo wild-type (WT) PTP1B to date is presented out of a total of ∼350 PTP1B structures in the PDB. This structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. The conformational differences between these chains are interrogated in the apo structure and between several recently reported high-resolution ligand-bound structures. Electron-density maps in a high-resolution structure of a recently reported activating double mutant are also examined, and unmodeled alternate conformations in the mutant structure are discovered that coincide with regions of enhanced conformational heterogeneity in the new WT structure. These results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, these new data and analysis provide a detailed view of the conformational ensemble of PTP1B and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function. Full Article text
is Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase By journals.iucr.org Published On :: 2024-05-01 Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation. Full Article text
is Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO By journals.iucr.org Published On :: 2024-05-29 Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the enzyme responsible for the first step of carbon dioxide (CO2) fixation in plants, which proceeds via the carboxylation of ribulose 1,5-biphosphate. Because of the enormous importance of this reaction in agriculture and the environment, there is considerable interest in the mechanism of fixation of CO2 by RuBisCO. Here, a serial synchrotron crystallography structure of spinach RuBisCO is reported at 2.3 Å resolution. This structure is consistent with earlier single-crystal X-ray structures of this enzyme and the results are a good starting point for a further push towards time-resolved serial synchrotron crystallography in order to better understand the mechanism of the reaction. Full Article text
is Preliminary X-ray diffraction and ligand-binding analyses of the N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv By journals.iucr.org Published On :: 2024-06-27 Mycobacterium tuberculosis can reside and persist in deep tissues; latent tuberculosis can evade immune detection and has a unique mechanism to convert it into active disease through reactivation. M. tuberculosis Rv1421 (MtRv1421) is a hypothetical protein that has been proposed to be involved in nucleotide binding-related metabolism in cell-growth and cell-division processes. However, due to a lack of structural information, the detailed function of MtRv1421 remains unclear. In this study, a truncated N-terminal domain (NTD) of MtRv1421, which contains a Walker A/B-like motif, was purified and crystallized using PEG 400 as a precipitant. The crystal of MtRv1421-NTD diffracted to a resolution of 1.7 Å and was considered to belong to either the C-centered monoclinic space group C2 or the I-centered orthorhombic space group I222, with unit-cell parameters a = 124.01, b = 58.55, c = 84.87 Å, β = 133.12° or a = 58.53, b = 84.86, c = 90.52 Å, respectively. The asymmetric units of the C2 or I222 crystals contained two or one monomers, respectively. In terms of the binding ability of MtRv1421-NTD to various ligands, uridine diphosphate (UDP) and UDP-N-acetylglucosamine significantly increased the melting temperature of MtRv1421-NTD, which indicates structural stabilization through the binding of these ligands. Altogether, the results reveal that a UDP moiety may be required for the interaction of MtRv1421-NTD as a nucleotide-binding protein with its ligand. Full Article text
is Structures of Brucella ovis leucine-, isoleucine-, valine-, threonine- and alanine-binding protein reveal a conformationally flexible peptide-binding cavity By journals.iucr.org Published On :: 2024-08-23 Brucella ovis is an etiologic agent of ovine epididymitis and brucellosis that causes global devastation in sheep, rams, goats, small ruminants and deer. There are no cost-effective methods for the worldwide eradication of ovine brucellosis. B. ovis and other protein targets from various Brucella species are currently in the pipeline for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), with the aim of identifying new therapeutic targets. Furthermore, the wealth of structures generated are effective tools for teaching scientific communication, structural science and biochemistry. One of these structures, B. ovis leucine-, isoleucine-, valine-, threonine- and alanine-binding protein (BoLBP), is a putative periplasmic amino acid-binding protein. BoLBP shares less than 29% sequence identity with any other structure in the Protein Data Bank. The production, crystallization and high-resolution structures of BoLBP are reported. BoLBP is a prototypical bacterial periplasmic amino acid-binding protein with the characteristic Venus flytrap topology of two globular domains encapsulating a large central cavity containing the peptide-binding region. The central cavity contains small molecules usurped from the crystallization milieu. The reported structures reveal the conformational flexibility of the central cavity in the absence of bound peptides. The structural similarity to other LBPs can be exploited to accelerate drug repurposing. Full Article text
is Crystallographic fragment screen of the c-di-AMP-synthesizing enzyme CdaA from Bacillus subtilis By journals.iucr.org Published On :: 2024-08-23 Crystallographic fragment screening has become a pivotal technique in structure-based drug design, particularly for bacterial targets with a crucial role in infectious disease mechanisms. The enzyme CdaA, which synthesizes an essential second messenger cyclic di-AMP (c-di-AMP) in many pathogenic bacteria, has emerged as a promising candidate for the development of novel antibiotics. To identify crystals suitable for fragment screening, CdaA enzymes from Streptococcus pneumoniae, Bacillus subtilis and Enterococcus faecium were purified and crystallized. Crystals of B. subtilis CdaA, which diffracted to the highest resolution of 1.1 Å, were used to perform the screening of 96 fragments, yielding data sets with resolutions spanning from 1.08 to 1.87 Å. A total of 24 structural hits across eight different sites were identified. Four fragments bind to regions that are highly conserved among pathogenic bacteria, specifically the active site (three fragments) and the dimerization interface (one fragment). The coordinates of the three active-site fragments were used to perform an in silico drug-repurposing screen using the OpenEye suite and the DrugBank database. This screen identified tenofovir, an approved drug, that is predicted to interact with the ATP-binding region of CdaA. Its inhibitory potential against pathogenic E. faecium CdaA has been confirmed by ITC measurements. These findings not only demonstrate the feasibility of this approach for identifying lead compounds for the design of novel antibacterial agents, but also pave the way for further fragment-based lead-optimization efforts targeting CdaA. Full Article text
is First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis By journals.iucr.org Published On :: 2024-09-26 Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9–5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed. Full Article text
is Ternary structure of Plasmodium vivax N-myristoyltransferase with myristoyl-CoA and inhibitor IMP-0001173 By journals.iucr.org Published On :: 2024-09-18 Plasmodium vivax is a major cause of malaria, which poses an increased health burden on approximately one third of the world's population due to climate change. Primaquine, the preferred treatment for P. vivax malaria, is contraindicated in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency, a common genetic cause of hemolytic anemia, that affects ∼2.5% of the world's population and ∼8% of the population in areas of the world where P. vivax malaria is endemic. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) conducted a structure–function analysis of P. vivax N-myristoyltransferase (PvNMT) as part of efforts to develop alternative malaria drugs. PvNMT catalyzes the attachment of myristate to the N-terminal glycine of many proteins, and this critical post-translational modification is required for the survival of P. vivax. The first step is the formation of a PvNMT–myristoyl–CoA binary complex that can bind to peptides. Understanding how inhibitors prevent protein binding will facilitate the development of PvNMT as a viable drug target. NMTs are secreted in all life stages of malarial parasites, making them attractive targets, unlike current antimalarials that are only effective during the plasmodial erythrocytic stages. The 2.3 Å resolution crystal structure of the ternary complex of PvNMT with myristoyl-CoA and a novel inhibitor is reported. One asymmetric unit contains two monomers. The structure reveals notable differences between the PvNMT and human enzymes and similarities to other plasmodial NMTs that can be exploited to develop new antimalarials. Full Article text
is Grazing-incidence small-angle neutron scattering at high pressure (HP-GISANS): a soft matter feasibility study on grafted brush films By journals.iucr.org Published On :: We present a demonstration of high-pressure grazing-incidence small-angle neutron scattering for soft matter thin films. The results suggest changes in water reorganization at different pressures. Full Article text
is A micro-beamstop with transmission detection by fluorescence for scanning-beam synchrotron scattering beamlines By journals.iucr.org Published On :: The correct determination of X-ray transmission at X-ray nanoprobes equipped with small beamstops for small- and wide-angle X-ray scattering collection is an unsolved problem with huge implications for data correction pipelines. We present a cost-effective solution to detect the transmission via the X-ray fluorescence of the beamstop with an avalanche photodiode. Full Article text
is Improving the reliability of small- and wide-angle X-ray scattering measurements of anisotropic precipitates in metallic alloys using sample rotation By journals.iucr.org Published On :: Rotations of small- and wide-angle X-ray scattering samples during acquisition are shown to give a drastic improvement in the reliability of the characterization of anisotropic precipitates in metallic alloys. Full Article text
is Multi-scale and time-resolved structure analysis of relaxor ferroelectric crystals under an electric field By journals.iucr.org Published On :: The electric field responses of the average and local lattice strains and polar nanoregions of relaxor ferroelectric PMN-30PT single crystals were revealed by multi-scale and time-resolved X-ray diffraction under DC and AC electric fields. Full Article text
is Towards expansion of the MATTS data bank with heavier elements: the influence of the wavefunction basis set on the multipole model derived from the wavefunction By journals.iucr.org Published On :: This study examines the quality of charge density obtained by fitting the multipole model to wavefunctions in different basis sets. The complex analysis reveals that changing the basis set quality from double- to triple-zeta can notably improve the charge density related properties of a multipole model. Full Article text
is Real-time analysis of liquid-jet sample-delivery stability for an X-ray free-electron laser using machine vision By journals.iucr.org Published On :: This paper describes real-time statistical analysis of liquid jet images for SFX experiments at the European XFEL. This analysis forms one part of the automated jet re-alignment system for SFX experiments at the SPB/SFX instrument of European XFEL. Full Article text
is Characterization and calibration of DECTRIS PILATUS3 X CdTe 2M high-Z hybrid pixel detector for high-precision powder diffraction measurements By journals.iucr.org Published On :: The performance of a high-Z photon-counting detector for powder diffraction measurements at high (>50 keV) energies is characterized, and the appropriate corrections are described in order to obtain data of higher quality than have previously been obtained from 2D detectors in these energy ranges. Full Article text
is RAPID, an ImageJ macro for indexing electron diffraction zone axis spot patterns of cubic materials By journals.iucr.org Published On :: RAPID (RAtio method Pattern InDexing) is an ImageJ macro script developed for the quick determination of sample orientation and indexing of calibrated and uncalibrated zone axis aligned electron diffraction patterns from materials with a cubic crystal structure. In addition to SAED and NBED patterns, the program is also capable of handling zone axis TEM Kikuchi patterns and FFTs derived from HR(S)TEM images. The software enables users to rapidly determine whether materials are cubic, pseudo-cubic, or non-cubic, and to distinguish between P, I, and F Bravais lattices. It can also provide lattice parameters for material verification and aid in determining the camera constant of the instrument, thus making the program a convenient tool for on-site crystallographic analysis in the TEM laboratory. Full Article text
is Advanced EXAFS analysis techniques applied to the L-edges of the lanthanide oxides By journals.iucr.org Published On :: The L-edge EXAFS of the entire set of lanthanide oxides were collected and modeled, taking into consideration the aggregation of inequivalent absorbing sites, geometric parameterization of the crystal lattice and multielectron excitation removal. Full Article text
is Multimodal reconstruction of TbCo thin-film structure with Bayesian analysis of polarized neutron reflectivity By journals.iucr.org Published On :: For the first time, a multimodal reconstruction of a magnetic thin-film structure has been found using polarised neutron reflectivity. This has been achieved by implementing the Bayesian approach in combination with error correction based on the maximum likelihood method and instrument function optimization. Full Article text
is Effect of thickness and noise on angular correlation analysis from scanning electron nanobeam diffraction of disordered carbon By journals.iucr.org Published On :: The impact of sample thickness and experimental noise on angular correlation analysis from scanning electron nanobeam diffraction patterns of disordered carbon are investigated and analyzed regarding the interpretability of the analysis results. Full Article text
is Crystal structure and Hirshfeld surface analysis of bis(benzoylacetonato)(ethanol)dioxidouranium(VI) By journals.iucr.org Published On :: In the complex, the ligand binds to the metal through an oxygen atom. The geometry of the seven-coordinate U atom is pentagonal bipyramidal, with the uranyl O atoms in apical positions. Full Article text
is Synthesis and structure of pentakis(2-aminopyridinium) nonavanado(V)tellurate(VI) By journals.iucr.org Published On :: In the title compound, the tellurium(VI) and vanadium(V) atoms are statistically disordered over two of the ten metal-atom sites in the unprotonated [TeV9O28]5– heteropolyanion. Full Article text
is Crystal structures and circular dichroism of {2,2'-[(1S,2S)-1,2-diphenylethane-1,2-diylbis(nitrilophenylmethanylylidene)]diphenolato}nickel(II) and its ethanol solvate By journals.iucr.org Published On :: A chiral nickel(II) Schiff base complex derived from 2-hydroxybenzophenone and (1S,2S)-1,2-diphenylethylenediamine shows a λ conformation of the central diamine chelate ring. The substituents on the C&z-dbnd;N carbon atoms significantly affect the circular dichroism spectra. Full Article text
is Crystal structure and Hirshfeld-surface analysis of an etoxazole metabolite designated R13 By journals.iucr.org Published On :: The crystal structure of a metabolite of the insecticide/acaricide etoxazole, designated R13 is presented along with a Hirshfeld surface analysis of intermolecular interactions present in the crystal structure. Full Article text
is Crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies of ethyl 5-amino-2-bromoisonicotinate By journals.iucr.org Published On :: Theoretical and experimental structural studies of the title compound were undertaken using X-ray and DFT methods. The interactions present in the crystal were analyzed using Hirshfeld surface and MEP surface analysis. Docking studies with a covid-19 main protease (PDB ID: 6LU7) as the target receptor indicate that the synthesized compound may be a potential candidate for pharmaceutical applications. Full Article text
is Crystal structure of a solvated dinuclear CuII complex derived from 3,3,3',3'-tetraethyl-1,1'-(furan-2,5-dicarbonyl)bis(thiourea) By journals.iucr.org Published On :: In the title compound, [Cu2(L)2]·2CH2Cl2, the CuII ions coordinate two (S,O)-chelating aroylthiourea moieties of doubly deprotonated furan-2,5-dicarbonylbis(N,N-diethylthiourea) (H2L) ligands. The coordination geometry of the metal centers is best described as a flat isosceles trapezoid with a cis arrangement of the donor atoms. Full Article text
is Synthesis, crystal structure and Hirshfeld surface analysis of N-(4-methoxyphenyl)picolinamide By journals.iucr.org Published On :: The molecular and crystal structure of N-(4-methoxyphenyl)picolinamide were studied and Hirshfeld surfaces and fingerprint plots were generated to investigate various intermolecular interactions. Full Article text
is Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1 By journals.iucr.org Published On :: N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 has a unique jellyfish-like structure with the prototypical macrophage migration inhibitory factor trimer as the `head' and a C-terminal extension as the `tail'. Full Article text
is A micro-beamstop with transmission detection by fluorescence for scanning-beam synchrotron scattering beamlines By journals.iucr.org Published On :: 2024-10-29 Quantitative X-ray diffraction approaches require careful correction for sample transmission. Though this is a routine task at state-of-the-art small-angle X-ray scattering (SAXS), wide-angle X-ray scattering (WAXS) or diffraction beamlines at synchrotron facilities, the transmission signal cannot be recorded concurrently with SAXS/WAXS when using the small, sub-millimetre beamstops at many X-ray nanoprobes during SAXS/WAXS experiments due to the divergence-limited size of the beamstop and the generally tight geometry. This is detrimental to the data quality and often the only solution is to re-scan the sample with a PIN photodiode as a detector to obtain transmission values. In this manuscript, we present a simple yet effective solution to this problem in the form of a small beamstop with an inlaid metal target for optimal fluorescence yield. This fluorescence can be detected with a high-sensitivity avalanche photodiode and provides a linear counter to determine the sample transmission. Full Article text