The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C15H22O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022). Powder Diffr. 37, 98–104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the inter­molecular inter­actions of germacrone type II.

In the title compound, {(C6H8N)[Zn2(HPO3)2(H2PO3)]}n, the constituent ZnO4, HPO3 and H2PO3 polyhedra of the inorganic component are linked into (010) sheets by Zn—O—P bonds (mean angle = 134.4°) and the layers are reinforced by O—H⋯O hydrogen bonds. The protonated templates are anchored to the inorganic sheets via bifurcated N—H⋯(O,O) hydrogen bonds.

The receptor ability of diethyl N,N'-(1,3-phenyl­ene)dicarbamate (1) to form host–guest com­plexes with theophylline (TEO) and caffeine (CAF) by mechanochemistry was evaluated. The formation of the 1–TEO com­plex (C12H16N2O4·C7H8N4O2) was preferred and involves the conformational change of one of the ethyl carbamate groups of 1 from the endo conformation to the exo conformation to allow the formation of inter­molecular inter­actions. The formation of an N—H⋯O=C hydrogen bond between 1 and TEO triggers the conformational change of 1. CAF mol­ecules are unable to form an N—H⋯O=C hydrogen bond with 1, making the conformational change and, therefore, the formation of the com­plex impossible. Conformational change and selective binding were monitored by IR spectroscopy, solid-state 13C nuclear magnetic resonance and single-crystal X-ray diffraction. The 1–TEO com­plex was characterized by IR spectroscopy, solid-state 13C nuclear magnetic resonance, powder X-ray diffraction and single-crystal X-ray diffraction.

By studying the structures of (μ-1,4,10,13-tetra­thia-7,16-di­aza­cyclo­octa­deca­ne)bis[iodidopalladium(II)] diiodide penta­(diiodine), [Pd2I2(C12H26N2S4)](I)2·5I2 or [Pd2I2([18]aneN2S4)](I)2·(I2)5, and 4,7,13,16,21,24-hexa­oxa-1,10-diazo­niabi­cyclo­[8.8.8]hexa­cosane triiodide iodide hemi­penta­(diiodine) di­chloro­methane mono­solvate, C18H38N2O62+·I3−·I−·2.5I2·CH2Cl2 or [H2([2.2.2]cryptand)](I3)(I)(I2)2.5·CH2Cl2, we confirm the structural variety of extended polyiodides achievable upon changing the shape, charge and dimensions of the cation template, by altering the synthetic strategy adopted and/or the experimental conditions. Although it is still often difficult to characterize discrete [I2m+n]n− polyiodides higher than I3− on the basis of structural parameters, such as I—I bond distances, FT–Raman spectroscopy appears to identify them as aggregates of I2, I− and (symmetric or slightly asymmetric) I3− building blocks linked by I⋯I inter­actions of varying strengths. However, because FT–Raman spectroscopy carries no information about the topological features of extended polyiodides, the two techniques should therefore be applied in combination to enhance the analysis of this kind of compounds.

The well-known copper car­box­yl­ate dimer, with four car­box­yl­ate ligands ex­ten­ding outwards towards the corners of a square, has been employed to generate a series of crystalline com­pounds. In particular, this work centres on the use of the 4-hy­droxy­benzoate anion (Hhba−) and its deprotonated phe­nol­ate form 4-oxidobenzoate (hba2−) to obtain complexes with the general formula [Cu2(Hhba)4–x(hba)xL2–y]x−, where L is an axial coligand (including solvent mol­ecules), x = 0, 1 or 2, and y = 0 or 1. In some cases, short hy­dro­gen bonds result in complexes which may be represented as [Cu2(Hhba)2(H0.5hba)2L2]−. The main focus of the investigation is on the formation of a variety of extended networks through hy­dro­gen bonding and, in some crystals, coordinate bonds when bridging coligands (L) are employed. Crystals of [Cu2(Hhba)4(di­ox­ane)2]·4(di­ox­ane) consist of the expected Cu dimer with the Hhba− anions forming hy­dro­gen bonds to 1,4-di­ox­ane mol­ecules which block network formation. In the case of crystals of com­position [Et4N][Cu2(Hhba)2(H0.5hba)2(CH3OH)(H2O)]·2(di­ox­ane), Li[Cu2(Hhba)2(H0.5hba)2(H2O)2]·3(di­ox­ane)·4H2O and [Cu2(Hhba)2(H0.5hba)2(H0.5DABCO)2]·3CH3OH (DABCO is 1,4-di­aza­bicyclo­[2.2.2]octa­ne), square-grid hy­dro­gen-bonded networks are generated in which the complex serves as one type of 4-con­necting node, whilst a second 4-con­necting node is a hy­dro­gen-bonding motif assembled from four phenol/phenolate groups. Another two-dimensional (2D) network based upon a related square-grid structure is formed in the case of [Et4N]2[Cu2(Hhba)2(hba)2(di­ox­ane)2][Cu2(Hhba)4(di­ox­ane)(H2O)]·CH3OH. In [Cu2(Hhba)4(H2O)2]·2(Et4NNO3), a square-grid structure is again apparent, but, in this case, a pair of nitrate anions, along with four phenolic groups and a pair of water mol­ecules, combine to form a second type of 4-con­necting node. When 1,8-bis­(di­methyl­amino)­naphthalene (bdn, `proton sponge') is used as a base, another square-grid network is generated, i.e. [Hbdn]2[Cu2(Hhba)2(hba)2(H2O)2]·3(di­ox­ane)·H2O, but with only the copper dimer complex serving as a 4-con­necting node. Complex three-dimensional networks are formed in [Cu2(Hhba)4(O-bipy)]·H2O and [Cu2(Hhba)4(O-bipy)2]·2(di­ox­ane), where the potentially bridging 4,4'-bi­pyridine N,N'-dioxide (O-bipy) ligand is employed. Rare cases of mixed car­box­yl­ate copper dimer complexes were obtained in the cases of [Cu2(Hhba)3(OAc)(di­ox­ane)]·3.5(di­ox­ane) and [Cu2(Hhba)2(OAc)2(DABCO)2]·10(di­ox­ane), with each structure possessing a 2D network structure. The final com­pound re­por­ted is a simple hy­dro­gen-bonded chain of com­position (H0.5DABCO)(H1.5hba), formed from the reaction of H2hba and DABCO.

Geminal and vicinal bis­(tri­fluoro­methane­sulfonate) esters are highly reactive alkyl­ene synthons used as potent electrophiles in the macrocyclization of imid­azoles and the transformation of bypyridines to diquat derivatives via nucleophilic substitution reactions. Herein we report the crystal structures of methyl­ene (C3H2F6O6S2) and ethyl­ene bis­(tri­fluoro­methane­sulfonate) (C4H4F6O6S2), the first examples of a geminal and vicinal bis­(tri­fluoro­methane­sulfonate) ester characterized by single-crystal X-ray diffraction (SC-XRD). With melting points slightly below ambient temperature, both reported bis­(tri­fluoro­methane­sulfonate)s are air- and moisture-sensitive oils and were crys­tallized at 277 K to afford two-com­ponent non-merohedrally twinned crystals. The dominant inter­actions present in both com­pounds are non-classical C—H⋯O hydrogen bonds and inter­molecular C—F⋯F—C inter­actions between tri­fluoro­methyl groups. Mol­ecular electrostatic potential (MEP) cal­culations by DFT-D3 helped to qu­antify the polarity between O⋯H and F⋯F contacts to rationalize the self-sorting of both bis­(tri­fluoro­methane­sulfonate) esters in polar (non-fluorous) and non-polar (fluorous) domains within the crystal structure.

The structure of cis- or trans-bridged [GeF5]− anionic chains have been investigated [Mallouk et al. (1984). Inorg. Chem. 23, 3160–3166] showing the first crystal structures of μ-F-bridged penta­fluoro­germanates. Herein, we report the second crystal structure of trans-penta­fluoro­germanate anions present in the crystal structure of sodium trans-penta­fluoro­germanate(IV) bis­(hy­dro­gen fluoride), Na[GeF5]·2HF. The crystal structure [ortho­rhom­bic Pca21, a = 12.3786 (3), b = 7.2189 (2), c = 11.4969 (3) Å and Z = 8] is built up from infinite chains of trans-linked [GeF6]2− octa­hedra, extending along the b axis and spanning a network of penta­gonal bipyramidal distorted Na-centred polyhedra. These [NaF7] polyhedra are linked in a trans-edge fashion via hy­dro­gen fluoride mol­ecules, in analogy to already known sodium hy­dro­gen fluorides and potassium hy­dro­gen fluorides.

The synthesis and structural characterization of four novel supra­molecular hy­dro­gen-bonded arrangements based on self-assembly from mol­ecular `[Cu(2,2'-bi­imid­az­ole)]' modules and malonate anions are pre­sent­ed, namely, tetra­kis­(2,2'-bi­imid­az­ole)di-μ-chlorido-dimal­on­atotricopper(II) penta­hydrate, [Cu3(C3H2O4)2Cl2(C6H6N4)4]·5H2O or [Cu(H2biim)2(μ-Cl)Cu0.5(mal)]2·5H2O, aqua­(2,2'-bi­imid­az­ole)­mal­on­atocopper(II) dihydrate, [Cu(C3H2O4)(C6H6N4)(H2O)]·2H2O or [Cu(H2biim)(mal)(H2O)]·2H2O, bis­[aqua­bis­(2,2'-bi­imid­az­ole)­cop­per(II)] di­mal­on­atodi­perchloratocopper(II) 2.2-hydrate, [Cu(C6H6N4)2(H2O)]2[Cu(C3H2O4)(ClO4)2]·2.2H2O or [Cu(H2biim)2(H2O)]2[Cu(mal)2(ClO4)2]·2.2H2O, and bis­(2,2'-bi­imid­az­ole)­copper(II) bis­[bis­(2,2'-bi­imid­az­ole)(2-carb­oxy­acetato)mal­on­atocopper(II)] tridecahydrate, [Cu(C6H6N4)2][Cu(C3H2O4)(C3H3O4)(C6H6N4)2]·13H2O or [Cu(H2biim)2][Cu(H2biim)2(Hmal)(mal)]2·13H2O. These as­sem­blies are characterized by self-com­plementary donor–acceptor mol­ecular inter­actions, demonstrating a recurrent and distinctive pattern of hy­dro­gen-bonding preferences among the carboxyl­ate, carb­oxy­lic acid and N—H groups of the coordinated 2,2'-bi­imid­az­ole and malonate ligands. Additionally, co­or­din­ation of the carboxyl­ate group with the metallic centre helps sustain re­mark­able supra­molecular assemblies, such as layers, helices, double helix columns or 3D channeled architectures, including mixed-metal com­plexes, into a single structure.

To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.

The validation of structural models obtained by macromolecular X-ray crystallography against experimental diffraction data, whether before deposition into the PDB or after, is typically carried out exclusively against the merged data that are eventually archived along with the atomic coordinates. It is shown here that the availability of unmerged reflection data enables valuable additional analyses to be performed that yield improvements in the final models, and tools are presented to implement them, together with examples of the results to which they give access. The first example is the automatic identification and removal of image ranges affected by loss of crystal centering or by excessive decay of the diffraction pattern as a result of radiation damage. The second example is the `reflection-auditing' process, whereby individual merged data items showing especially poor agreement with model predictions during refinement are investigated thanks to the specific metadata (such as image number and detector position) that are available for the corresponding unmerged data, potentially revealing previously undiagnosed instrumental, experimental or processing problems. The third example is the calculation of so-called F(early) − F(late) maps from carefully selected subsets of unmerged amplitude data, which can not only highlight the location and extent of radiation damage but can also provide guidance towards suitable fine-grained parametrizations to model the localized effects of such damage.

Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.

The Swiss Light Source facilitates fragment-based drug-discovery campaigns for academic and industrial users through the Fast Fragment and Compound Screening (FFCS) software suite. This framework is further enriched by the option to utilize the Smart Digital User (SDU) software for automated data collection across the PXI, PXII and PXIII beamlines. In this work, the newly developed HEIDI webpage (https://heidi.psi.ch) is introduced: a platform crafted using state-of-the-art software architecture and web technologies for sample management of rotational data experiments. The HEIDI webpage features a data-review tab for enhanced result visualization and provides programmatic access through a representational state transfer application programming interface (REST API). The migration of the local FFCS MongoDB instance to the cloud is highlighted and detailed. This transition ensures secure, encrypted and consistently accessible data through a robust and reliable REST API tailored for the FFCS software suite. Collectively, these advancements not only significantly elevate the user experience, but also pave the way for future expansions and improvements in the capabilities of the system.

Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections and, in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image-processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species and classify different conformational states. Here, STOPGAP, an open-source package for subtomogram averaging that is designed to provide users with fine control over each of these steps, is described. In providing detailed descriptions of the image-processing algorithms that STOPGAP uses, this manuscript is also intended to serve as a technical resource to users as well as for further community-driven software development.

Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.

The detection of specific biological macromolecules in cryogenic electron tomography data is frequently approached by applying cross-correlation-based 3D template matching. To reduce computational cost and noise, high binning is used to aggregate voxels before template matching. This remains a prevalent practice in both practical applications and methods development. Here, the relation between template size, shape and angular sampling is systematically evaluated to identify ribosomes in a ground-truth annotated data set. It is shown that at the commonly used binning, a detailed subtomogram average, a sphere and a heart emoji result in near-identical performance. These findings indicate that with current template-matching practices macromolecules can only be detected with high precision if their shape and size are sufficiently different from the background. Using theoretical considerations, the experimental results are rationalized and it is discussed why primarily low-frequency information remains at high binning and that template matching fails to be accurate because similarly shaped and sized macromolecules have similar low-frequency spectra. These challenges are discussed and potential enhancements for future template-matching methodologies are proposed.

Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hit-to-lead development as they often establish halogen bonds with target proteins, potentially enhancing binding affinity and selectivity, as well as counteracting drug resistance. Here, the aim was to unambiguously identify the binding orientations of fragment hits for SARS-CoV-2 nonstructural protein 1 (nsp1) which contain a combination of sulfur and/or chlorine, bromine and iodine substituents. The binding orientations of carefully selected nsp1 analogue hits were focused on by employing their anomalous scattering combined with Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from the diffraction data collected at both standard and long-wavelength X-rays were compared. The discrepancies observed in the maps of iodine-containing fragments collected at different energies were attributed to site-specific radiation-damage stemming from the strong X-ray absorption of I atoms, which is likely to cause cleavage of the C—I bond. A reliable and effective data-collection strategy to unambiguously determine the binding orientations of low-occupancy fragments containing sulfur and/or halogen atoms while mitigating radiation damage is presented.

Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nɛ—H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1—H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C—H⋯O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C—H group. Consequently, Cα—H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cɛ1—H and Cδ2—H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1—H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1—H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5–3.0 kcal mol−1, depending on the specific stereochemistry.

Protein crystallography is an established method to study the atomic structures of macromolecules and their complexes. A prerequisite for successful structure determination is diffraction-quality crystals, which may require extensive optimization of both the protein and the conditions, and hence projects can stretch over an extended period, with multiple users being involved. The workflow from crystallization and crystal treatment to deposition and publication is well defined, and therefore an electronic laboratory information management system (LIMS) is well suited to management of the data. Completion of the project requires key information on all the steps being available and this information should also be made available according to the FAIR principles. As crystallized samples are typically shipped between facilities, a key feature to be captured in the LIMS is the exchange of metadata between the crystallization facility of the home laboratory and, for example, synchrotron facilities. On completion, structures are deposited in the Protein Data Bank (PDB) and the LIMS can include the PDB code in its database, completing the chain of custody from crystallization to structure deposition and publication. A LIMS designed for macromolecular crystallography, IceBear, is available as a standalone installation and as a hosted service, and the implementation of key features for the capture of metadata in IceBear is discussed as an example.

The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins. FeSII is an adrenodoxin-type ferredoxin that forms a dimer in solution. Previously, the crystal structure was solved [Schlesier et al. (2016), J. Am. Chem. Soc. 138, 239–247] with five copies in the asymmetric unit. One copy is a normal adrenodoxin domain that forms a dimer with its crystallographic symmetry mate. The other four copies are in an `open' conformation with a loop flipped out exposing the 2Fe–2S cluster. The open and closed conformations were interpreted as oxidized and reduced, respectively, and the large conformational change in the open configuration allowed binding to nitrogenase. Here, the structure of FeSII was independently solved in the same crystal form. The positioning of the atoms in the unit cell is similar to the earlier report. However, the interpretation of the structure is different. The `open' conformation is interpreted as the product of a crystallization-induced domain swap. The 2Fe–2S cluster is not exposed to solvent, but in the crystal its interacting helix is replaced by the same helix residues from a crystal symmetry mate. The domain swap is complicated, as it is unusual in being in the middle of the protein rather than at a terminus, and it creates arrangements of molecules that can be interpreted in multiple ways. It is also cautioned that crystal structures should be interpreted in terms of the contents of the entire crystal rather than of one asymmetric unit.

The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE–fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.

Several proteins from plant pathogenesis-related family 10 (PR10) are highly abundant in the latex of opium poppy and have recently been shown to play diverse and important roles in the biosynthesis of benzylisoquinoline alkaloids (BIAs). The recent determination of the first crystal structures of PR10-10 showed how large conformational changes in a surface loop and adjacent β-strand are coupled to the binding of BIA compounds to the central hydrophobic binding pocket. A more detailed analysis of these conformational changes is now reported to further clarify how ligand binding is coupled to the formation and cleavage of an intermolecular disulfide bond that is only sterically allowed when the BIA binding pocket is empty. To decouple ligand binding from disulfide-bond formation, each of the two highly conserved cysteine residues (Cys59 and Cys155) in PR10-10 was replaced with serine using site-directed mutagenesis. Crystal structures of the Cys59Ser mutant were determined in the presence of papaverine and in the absence of exogenous BIA compounds. A crystal structure of the Cys155Ser mutant was also determined in the absence of exogenous BIA compounds. All three of these crystal structures reveal conformations similar to that of wild-type PR10-10 with bound BIA compounds. In the absence of exogenous BIA compounds, the Cys59Ser and Cys155Ser mutants appear to bind an unidentified ligand or mixture of ligands that was presumably introduced during expression of the proteins in Escherichia coli. The analysis of conformational changes triggered by the binding of BIA compounds suggests a molecular mechanism coupling ligand binding to the disruption of an intermolecular disulfide bond. This mechanism may be involved in the regulation of biosynthetic reactions in plants and possibly other organisms.

A key prerequisite for the successful application of protein crystallography in drug discovery is to establish a robust crystallization system for a new drug-target protein fast enough to deliver crystal structures when the first inhibitors have been identified in the hit-finding campaign or, at the latest, in the subsequent hit-to-lead process. The first crucial step towards generating well folded proteins with a high likelihood of crystallizing is the identification of suitable truncation variants of the target protein. In some cases an optimal length variant alone is not sufficient to support crystallization and additional surface mutations need to be introduced to obtain suitable crystals. In this contribution, four case studies are presented in which rationally designed surface modifications were key to establishing crystallization conditions for the target proteins (the protein kinases Aurora-C, IRAK4 and BUB1, and the KRAS–SOS1 complex). The design process which led to well diffracting crystals is described and the crystal packing is analysed to understand retrospectively how the specific surface mutations promoted successful crystallization. The presented design approaches are routinely used in our team to support the establishment of robust crystallization systems which enable structure-guided inhibitor optimization for hit-to-lead and lead-optimization projects in pharmaceutical research.

Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operations and record-keeping of a scientific facility, has been introduced. EMhub enables the easy management of user information, instruments, bookings and projects. The application was initially developed to meet the needs of a cryoEM facility, but its functionality and adaptability have proven to be broad enough to be extended to other data-generating centers. The expansion of EMHub is enabled by the modular nature of its core functionalities. The application allows external processes to be connected via a REST API, automating tasks such as folder creation, user and password generation, and the execution of real-time data-processing pipelines. EMhub has been used for several years at the Swedish National CryoEM Facility and has been installed in the CryoEM center at the Structural Biology Department at St. Jude Children's Research Hospital. A fully automated single-particle pipeline has been implemented for on-the-fly data processing and analysis. At St. Jude, the X-Ray Crystallography Center and the Single-Molecule Imaging Center have already expanded the platform to support their operational and data-management workflows.

Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0.012 (7) Å for the refinement on diffuse scattering in single-crystal X-ray diffraction data and 0.03 (2) Å for the refinement on the diffuse scattering in single-crystal electron diffraction data. As electron diffraction requires much smaller crystals than X-ray diffraction, this opens up the possibility of refining short-range order parameters in many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.

Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB–TcC subcomplex that makes a hollow shell. This TcB–TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB–TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.

This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.

In this work, regenerated cellulose textile fibers, Ioncell-F, dry-wet spun with different draw ratios, have been investigated by scanning wide-angle X-ray scattering (WAXS) using a mesoscopic X-ray beam. The fibers were found to be homogeneous on the 500 nm length scale. Analysis of the azimuthal angular dependence of a crystalline Bragg spot intensity revealed a radial dependence of the degree of orientation of crystallites that was found to increase with the distance from the center of the fiber. We attribute this to radial velocity gradients during the extrusion of the spin dope and the early stage of drawing. On the other hand, the fiber crystallinity was found to be essentially homogeneous over the fiber cross section.

Investigation of the analyte soaking conditions on the crystalline sponge {[(ZnI2)3(tpt)2·x(solvent)]n} method using a statistical design of experiments model has provided fundamental insights into the influence of experimental variables. This approach focuses on a single analyte tested via 60 experiments (20 unique conditions) to identify the main effects for success and overall guest structure quality. This is employed as a basis for the development of a novel molecular structure grading system that enables the quantification of guest exchange quality.

X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump–probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light–oxygen–voltage domain 1 (LOV1) from Chlamydomonas reinhardtii were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump–probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δt = 10 µs a covalent thio­ether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.

The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, especially where the experimental data are of limited resolution. A novel protein structure validation approach based on spotting inconsistencies between the residue contacts and distances observed in a structural model and those computationally predicted by methods such as AlphaFold2 has previously been established. It is particularly well suited to the detection of register errors. Importantly, this new approach is orthogonal to traditional methods based on stereochemistry or map–model agreement, and is resolution independent. Here, thousands of likely register errors are identified by scanning 3–5 Å resolution structures in the PDB. Unlike most methods, the application of this approach yields suggested corrections to the register of affected regions, which it is shown, even by limited implementation, lead to improved refinement statistics in the vast majority of cases. A few limitations and confounding factors such as fold-switching proteins are characterized, but this approach is expected to have broad application in spotting potential issues in current accessions and, through its implementation and distribution in CCP4, helping to ensure the accuracy of future depositions.

Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and, therefore, explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine-learning methods that employ low-dimensional latent space representations. The non-linear nature of many of these methods poses a challenge to their validation and interpretation and to identifying functionally relevant conformational trajectories. These methods would benefit from in-depth benchmarking using high-quality synthetic data and concomitant ground truth information. We present a framework for the simulation and subsequent analysis with respect to the ground truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. These synthetic data can be processed as if they were experimental data, allowing aspects of standard SPA workflows as well as heterogeneous reconstruction methods to be compared with known ground truth using available utilities. The simulation and analysis of several such datasets are demonstrated and an initial investigation into HRAs is presented.

The interaction of intense synchrotron radiation with molecular crystals frequently modifies the crystal structure by breaking bonds, producing fragments and, hence, inducing disorder. Here, a second-rank tensor of radiation-induced lattice strain is proposed to characterize the structural susceptibility to radiation. Quantitative estimates are derived using a linear response approximation from experimental data collected on three materials Hg(NO3)2(PPh3)2, Hg(CN)2(PPh3)2 and BiPh3 [PPh3 = triphenylphosphine, P(C6H5)3; Ph = phenyl, C6H5], and are compared with the corresponding thermal expansivities. The associated eigenvalues and eigenvectors show that the two tensors are not the same and therefore probe truly different structural responses. The tensor of radiative expansion serves as a measure of the susceptibility of crystal structures to radiation damage.

SnGe4N4O4 was synthesized at high pressure (16 and 20 GPa) and high temperature (1200 and 1500°C) in a large-volume press. Powder X-ray diffraction experiments using synchrotron radiation indicate that the derived samples are mixtures of known and unknown phases. However, the powder X-ray diffraction patterns are not sufficient for structural characterization. Transmission electron microscopy studies reveal crystals of several hundreds of nanometres in size with different chemical composition. Among them, crystals of a previously unknown phase with stoichiometry SnGe4N4O4 were detected and investigated using automated diffraction tomography (ADT), a three-dimensional electron diffraction method. Via ADT, the crystal structure could be determined from single nanocrystals in space group P63mc, exhibiting a nolanite-type structure. This was confirmed by density functional theory calculations and atomic resolution scanning transmission electron microscopy images. In one of the syntheses runs a rhombohedral 6R polytype of SnGe4N4O4 could be found together with the nolanite-type SnGe4N4O4. The structure of this polymorph was solved as well using ADT.

Thio­phosgene is one of the principal C=S building blocks in synthetic chemistry. At room temperature, thio­phosgene is a red liquid. While its properties in the liquid and gaseous states are well known, a comprehensive characterization of thio­phosgene in its solid state is presented here. Differential scanning calorimetry shows that thio­phosgene forms a supercooled melt before rapidly crystallizing. Its melting point is 231.85 K (−41.3 °C). At 80 K, thio­phosgene crystallizes in space group P63/m [No. 174, a = b = 5.9645 (2), c = 6.2835 (3) Å, V = 193.59 (2) Å3]. The molecule shows a distinct rotational disorder: all S and Cl positions are of mixed occupancy and the disorder does not resolve at temperatures as low as 10 K, as was shown by neutron powder diffraction. Infrared, Raman and inelastic neutron scattering spectra were collected and assigned with the aid of quantum chemical calculations. A larger ordered structural model allowed for better agreement between the measured and calculated spectra, further indicating that disorder is an inherent feature of solid-state thio­phosgene.

Onchocerca volvulus causes blindness, onchocerciasis, skin infections and devastating neurological diseases such as nodding syndrome. New treatments are needed because the currently used drug, ivermectin, is contraindicated in pregnant women and those co-infected with Loa loa. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) produced, crystallized and determined the apo structure of N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 (His-OvMIF-1). OvMIF-1 is a possible drug target. His-OvMIF-1 has a unique jellyfish-like structure with a prototypical macrophage migration inhibitory factor (MIF) trimer as the `head' and a unique C-terminal `tail'. Deleting the N-terminal tag reveals an OvMIF-1 structure with a larger cavity than that observed in human MIF that can be targeted for drug repurposing and discovery. Removal of the tag will be necessary to determine the actual biological oligomer of OvMIF-1 because size-exclusion chomatographic analysis of His-OvMIF-1 suggests a monomer, while PISA analysis suggests a hexamer stabilized by the unique C-terminal tails.

The ternary magnesium/lithium boride, MgxLi3 − xB48 − y (x = 1.11, y = 0.40, idealized formula MgLi2B48), crystallizes as its own structure type in P43212, which is closely related to the structural family comprising α-AlB12, Be0.7Al1.1B22 and tetra­gonal β-boron. The asymmetric unit of title structure contains two statistical mixtures Mg/Li in Wyckoff sites 8b with relative occupancies Mg:Li = 0.495 (9):0.505 (9) and 4a with Mg:Li = 0.097 (8):0.903 (8). The boron atoms occupy 23 8b sites and two 4a sites. One of the latter sites has a partial occupancy factor of 0.61 (2). Both unique Mg/Li atoms adopt a twelvefold coordination environment in the form of truncated tetra­hedra (Laves polyhedra). These polyhedra are connected by triangular faces to four [B12] icosa­hedra. The boron atoms exhibit four kinds of polyhedra, namely penta­gonal pyramid (coordination number CN = 6), distorted tetra­gonal pyramid (CN = 5), bicapped hexa­gon (CN = 8) and gyrobifastigium (CN = 8). At the gas hydrogenation of MgLi2B48 alloy, formation of the eutectic composite hydride LiBH4+Mg(BH4)2 and amorphous boron is observed. In the temperature range 543–623 K, the hydride eutectics decompose, forming MgH2, LiH, MgB4, B and H2.

The structures of 16 phosphane chalcogenide complexes of gold(I) halides, with the general formula R13-nR2nPEAuX (R1 = t-butyl; R2 = isopropyl; n = 0 to 3; E = S or Se; X = Cl, Br or I), are presented. The eight possible chlorido derivatives are: 1a, n = 3, E = S; 2a, n = 2, E = S; 3a, n = 1, E = S; 4a, n = 0, E = S; 5a, n = 3, E = Se; 6a, n = 2, E = Se; 7a, n = 1, E = Se; and 8a, n = 0, E = Se, and the corresponding bromido derivatives are 1b–8b in the same order. However, 2a and 2b were badly disordered and 8a was not obtained. The iodido derivatives are 2c, 6c and 7c (numbered as for the series a and b). All structures are solvent-free and all have Z' = 1 except for 6b and 6c (Z' = 2). All mol­ecules show the expected linear geometry at gold and approximately tetra­hedral angles P—E—Au. The presence of bulky ligands forces some short intra­molecular contacts, in particular H⋯Au and H⋯E. The Au—E bond lengths have a slight but consistent tendency to be longer when trans to a softer X ligand, and vice versa. The five compounds 1a, 5a, 6a, 1b and 5b form an isotypic set, despite the different alkyl groups in 6a. Compounds 3a/3b, 4b/8b and 6b/6c form isotypic pairs. The crystal packing can be analysed in terms of various types of secondary inter­actions, of which the most frequent are `weak' hydrogen bonds from methine hydrogen atoms to the halogenido ligands. For the structure type 1a, H⋯X and H⋯E contacts combine to form a layer structure. For 3a/3b, the packing is almost featureless, but can be described in terms of a double-layer structure involving borderline H⋯Cl/Br and H⋯S contacts. In 4a and 4b/8b, which lack methine groups, Cmeth­yl—H⋯X contacts combine to form layer structures. In 7a/7b, short C—H⋯X inter­actions form chains of mol­ecules that are further linked by association of short Au⋯Se contacts to form a layer structure. The packing of compound 6b/6c can conveniently be analysed for each independent mol­ecule separately, because they occupy different regions of the cell. Mol­ecule 1 forms chains in which the mol­ecules are linked by a Cmethine⋯Au contact. The mol­ecules 2 associate via a short Se⋯Se contact and a short H⋯X contact to form a layer structure. The packing of compound 2c can be described in terms of two short Cmethine—H⋯I contacts, which combine to form a corrugated ribbon structure. Compound 7c is the only compound in this paper to feature Au⋯Au contacts, which lead to twofold-symmetric dimers. Apart from this, the packing is almost featureless, consisting of layers with only translation symmetry except for two very borderline Au⋯H contacts.

Since its founding in 2013, the Young Crystallographers (YC) have become one of the most active working groups not only within their parent organization, the German Crystallographic Society (DGK), but also among other young crystallographers' groups in Europe and the world. The aim of the YC is and always has been to support early-career researchers in the diverse fields of crystallography and the rejuvenation of the field on a national scale. Over the past decade, we have curated events, platforms, and educational content tailored to foster collaboration and knowledge transfer among young crystallographers. In this article, we introduce our group and show how this active and diverse community has shaped the rejuvenation of crystallography in Germany, strengthened by the support of our national society.

The structures of ten phosphane chalcogenide complexes of gold(III) halides, with general formula R13–nR2nPEAuX3 (R1 = t-butyl; R2 = i-propyl; n = 0 to 3; E = S or Se; X = Cl or Br) are presented. The eight possible chlorido derivatives are: 9a, n = 3, E = S; 10a, n = 2, E = S; 11a, n = 1, E = S; 12a, n = 0, E = S; 13a, n = 3, E = Se; 14a, n = 2, E = Se; 15a, n = 1, E = Se; and 16a, n = 0, E = Se, and the corresponding bromido derivatives are 9b–16b in the same order. Structures were obtained for 9a, 10a (and a second polymorph 10aa), 11a (and its deutero­chloro­form monosolvate 11aa), 12a (as its di­chloro­methane monosolvate), 14a, 15a (as its deutero­chloro­form monosolvate 15aa, in which the solvent mol­ecule is disordered over two positions), 9b, 11b, 13b and 15b. The structures of 11a, 15a, 11b and 15b form an isotypic set, and those of compounds 10aa and 14a form an isotypic pair. All structures have Z' = 1. The gold(III) centres show square-planar coordination geometry and the chalcogenide atoms show approximately tetra­hedral angles (except for the very wide angle in 12a, probably associated with the bulky t-butyl groups). The bond lengths at the gold atoms are lengthened with respect to the known gold(I) derivatives, and demonstrate a considerable trans influence of S and Se donor atoms on a trans Au—Cl bond. Each compound with an isopropyl group shows a short intra­molecular contact of the type C—Hmethine⋯Xcis; these may be regarded as intra­molecular ‘weak’ hydrogen bonds, and they determine the orientation of the AuX3 groups. The mol­ecular packing is analysed in terms of various short contacts such as weak hydrogen bonds C—H⋯X and contacts between the heavier atoms, such as X⋯X (9a, 10aa, 11aa, 15aa and 9b), S⋯S (10aa, 11a and 12a) and S⋯Cl (10a). The packing of the polymorphs 10a and 10aa is thus quite different. The solvent mol­ecules take part in C—H⋯Cl hydrogen bonds; for 15aa, a disordered solvent region at z ≃ 0 is observed. Structure 13b involves unusual inversion-symmetric dimers with Se⋯Au and Se⋯Br contacts, further connected by Br⋯Br contacts.

The structures of fourteen halochalcogenyl­phospho­nium tetra­halogen­ido­aurates(III), phosphane chalcogenide derivatives with general formula [R13–nR2nPEX][AuX4] (R1 = t-butyl; R2 = isopropyl; n = 0 to 3; E = S or Se; X = Cl or Br) are presented. The eight possible chlorido derivatives are: 17a, n = 3, E = S; 18a, n = 2, E = S; 19a, n = 1, E = S; 20a, n = 0, E = S; 21a, n = 3, E = Se; 22a, n = 2, E = Se; 23a, n = 1, E = Se; and 24a, n = 0, E = Se, and the corresponding bromido derivatives are 17b–24b in the same order. Structures were obtained for all compounds except for the tri-t-butyl derivatives 24a and 24b. Isotypy is observed for 18a/18b/22a/22b, 19a/23a, 17b/21b and 19b/23b. In eleven of the compounds, X⋯X contacts (mostly very short) are observed between the cation and anion, whereby the E—X⋯X groups are approximately linear and the X⋯X—Au angles approximately 90°. The exceptions are 17a, 19a and 23a, which instead display short E⋯X contacts. Bond lengths in the cations correspond to single bonds P—E and E—X. For each group with constant E and X, the P—E—X bond-angle values increase monotonically with the steric bulk of the alkyl groups. The packing is analysed in terms of E⋯X, X⋯X (some between anions alone), H⋯X and H⋯Au contacts. Even for isotypic compounds, some significant differences can be discerned.

The crystal structure of the title 2:1 mol­ecular complex between 2-(allyl­thio)­pyridine and 1,2,4,5-tetra­fluoro-3,6-di­iodo­benzene, C6F4I2·2C8H9NS, at 100 K has been determined in the monoclinic space group P21/c. The most noteworthy characteristic of the complex is the halogen bond between iodine and the pyridine ring with a short N⋯I contact [2.8628 (12) Å]. The Hirshfeld surface analysis shows that the hydrogen⋯hydrogen contacts dominate the crystal packing with a contribution of 32.1%.

Single crystals of the mol­ecular compound, {Cu20Ir6Cl8(C21H24N2)6(C4H4N2)3]·3.18CH3OH or [({Cu10Ir3}Cl4(IMes)3(pyrazine))2(pyrazine)]·3.18CH3OH [where IMes is 1,3-bis­(2,4,6-trimethylphen­yl)imidazol-2-yl­idene], with a unique heterometallic cluster have been prepared and the structure revealed using single-crystal X-ray diffraction. The mol­ecule is centrosymmetric with two {Cu10Ir3} cores bridged by a pyrazine ligand. The polymetallic cluster contains three stabilizing N-heterocyclic carbenes, four Cl ligands, and a non-bridging pyrazine ligand. Notably, the Cu—Ir core is arranged in an unusual shape containing 13 vertices, 22 faces, and 32 sides. The atoms within the trideca­metallic cluster are arranged in four planes, with 2, 4, 4, 3 metals in each plane. Ir atoms are present in alternate planes with an Ir atom featuring in the peripheral bimetallic plane, and two Ir atoms featuring on opposite sides of the non-adjacent tetra­metallic plane. The crystal contains two disordered methanol solvent mol­ecules with an additional region of non-modelled electron density corrected for using the SQUEEZE routine in PLATON [Spek (2015). Acta Cryst. C71, 9–18]. The given chemical formula and other crystal data do not take into account the unmodelled methanol solvent mol­ecule(s).

In the title compound, C10H8N2·2C6H5NO3, 4-nitro­phenol and 4,4'-bi­pyridine crystallized together in a 2:1 ratio in the space group P21/n. There is a hydrogen-bonding inter­action between the nitro­gen atoms on the 4,4'-bi­pyridine mol­ecule and the hydrogen atom on the hydroxyl group on the 4-nitro­phenol, resulting in trimolecular units. This structure is a polymorph of a previously reported structure [Nayak & Pedireddi (2016). Cryst. Growth Des. 16, 5966–5975], which differs mainly due to a twist in the 4,4'-bi­pyridine mol­ecule.

In the title salt, C6H16N22+ ·H2P2O72−, the complete dication is generated by a crystallographic centre of symmetry with the methyl groups in equatorial orientations. The complete dianion is generated by a crystallographic twofold axis with the central O atom lying on the axis: the P—O—P bond angle is 135.50 (12)°. In the crystal, the di­hydrogen diphosphate anions are linked by O—H⋯O hydrogen bonds, generating (001) layers. The organic cations bond to the inorganic layers by way of N—H⋯O and C—H⋯O hydrogen bonds. A Hirshfeld surface analysis shows that the most important contributions for the crystal packing are from O⋯H/H⋯O (60.5%) and H⋯H (39.4%) contacts.

In this work, we showed that the use of ethanol to increase image contrast when imaging cardiac tissue with synchrotron X-ray phase-contrast imaging (X-PCI) leads to heterogeneous tissue shrinkage, which has an impact on the 3D organization of the myocardium.

X-ray absorption spectroscopy (XAS) is a promising technique for determining structural information from sensitive biological samples, but high-accuracy X-ray absorption fine structure (XAFS) requires corrections of systematic errors in experimental data. Low-temperature XAS and room-temperature X-ray absorption spectro-electrochemical (XAS-EC) measurements of N-truncated amyloid-β samples were collected and corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumber (k). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing.

Hendrickson & Lattman [Acta Cryst. (1970), B26, 136–143] introduced a method for representing crystallographic phase probabilities defined on the unit circle. Their approach could model the bimodal phase probability distributions that can result from experimental phase determination procedures. It also provided simple and highly effective means to combine independent sources of phase information. The present work discusses the equivalence of the Hendrickson–Lattman distribution and the generalized von Mises distribution of order two, which has been studied in the statistical literature. Recognizing this connection allows the Hendrickson–Lattman distribution to be expressed in an alternative form which is easier to interpret, as it involves the location and concentration parameters of the component von Mises distributions. It also allows clarification of the conditions for bimodality and access to a simplified analytical method for evaluating the trigonometric moments of the distribution, the first of which is required for computing the best Fourier synthesis in the presence of phase, but not amplitude, uncertainty.

NdGa hydride and deuteride phases were prepared from high-quality NdGa samples and their structures characterized by powder and single-crystal X-ray diffraction and neutron powder diffraction. NdGa with the orthorhombic CrB-type structure absorbs hydrogen at hydrogen pressures ≤ 1 bar until reaching the composition NdGaH(D)1.1, which maintains a CrB-type structure. At elevated hydrogen pressure additional hydrogen is absorbed and the maximum composition recovered under standard temperature and pressure conditions is NdGaH(D)1.6 with the Cmcm LaGaH1.66-type structure. This structure is a threefold superstructure with respect to the CrB-type structure. The hydrogen atoms are ordered and distributed on three fully occupied Wyckoff positions corresponding to tetrahedral (4c, 8g) and trigonal–bipyramidal (8g) voids in the parent structure. The threefold superstructure is maintained in the H-deficient phases NaGaH(D)x until 1.6 ≥ x ≥ 1.2. At lower H concentrations, coinciding with the composition of the hydride obtained from hydrogenation at atmospheric pressure, the unit cell of the CrB-type structure is resumed. This phase can also display H deficiency, NdGaH(D)y (1.1 ≥ y ≥ 0.9), with H(D) exclusively situated in partially empty tetrahedral voids. The phase boundary between the threefold superstructure (LaGaH1.66 type) and the onefold structure (NdGaH1.1 type) is estimated on the basis of phase–composition isotherms and neutron powder diffraction to be x = 1.15.

The maximum range of perpendicular momentum transfer (qz) has been tripled for X-ray scattering from liquid surfaces when using a double-crystal deflector setup to tilt the incident X-ray beam. This is achieved by employing a higher-energy X-ray beam to access Miller indices of reflecting crystal atomic planes that are three times higher than usual. The deviation from the exact Bragg angle condition induced by misalignment between the X-ray beam axis and the main rotation axis of the double-crystal deflector is calculated, and a fast and straightforward procedure to align them is deduced. An experimental method of measuring scattering intensity along the qz direction on liquid surfaces up to qz = 7 Å−1 is presented, with liquid copper serving as a reference system for benchmarking purposes.