all Validation of electron-microscopy maps using solution small-angle X-ray scattering By journals.iucr.org Published On :: 2024-06-27 The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear resonance methods, but during the last decade, cryogenic transmission electron microscopy (cryo-TEM) has become an equally important tool. As the blotting and flash-freezing of the samples can induce conformational changes, external validation tools are required to ensure that the vitrified samples are representative of the solution. Although many validation tools have already been developed, most of them rely on fully resolved atomic models, which prevents early screening of the cryo-TEM maps. Here, a novel and automated method for performing such a validation utilizing small-angle X-ray scattering measurements, publicly available through the new software package AUSAXS, is introduced and implemented. The method has been tested on both simulated and experimental data, where it was shown to work remarkably well as a validation tool. The method provides a dummy atomic model derived from the EM map which best represents the solution structure. Full Article text
all A snapshot love story: what serial crystallography has done and will do for us By journals.iucr.org Published On :: 2024-07-10 Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique in structural biology. Initially pioneered at X-ray free-electron laser facilities, it has now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments in serial crystallography, emphasizing recent results in time-resolved crystallography, and discussing challenges and shortcomings. Full Article text
all Managing macromolecular crystallographic data with a laboratory information management system By journals.iucr.org Published On :: 2024-07-10 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. Full Article text
all Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them By journals.iucr.org Published On :: 2024-07-16 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. Full Article text
all Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals By journals.iucr.org Published On :: 2024-07-25 Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from cryo-cooled crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CLpro, Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures. Full Article text
all Surface-mutagenesis strategies to enable structural biology crystallization platforms By journals.iucr.org Published On :: 2024-08-29 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. Full Article text
all Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy By journals.iucr.org Published On :: 2024-10-01 During the automatic processing of crystallographic diffraction experiments, beamstop shadows are often unaccounted for or only partially masked. As a result of this, outlier reflection intensities are integrated, which is a known issue. Traditional statistical diagnostics have only limited effectiveness in identifying these outliers, here termed Not-Excluded-unMasked-Outliers (NEMOs). The diagnostic tool AUSPEX allows visual inspection of NEMOs, where they form a typical pattern: clusters at the low-resolution end of the AUSPEX plots of intensities or amplitudes versus resolution. To automate NEMO detection, a new algorithm was developed by combining data statistics with a density-based clustering method. This approach demonstrates a promising performance in detecting NEMOs in merged data sets without disrupting existing data-reduction pipelines. Re-refinement results indicate that excluding the identified NEMOs can effectively enhance the quality of subsequent structure-determination steps. This method offers a prospective automated means to assess the efficacy of a beamstop mask, as well as highlighting the potential of modern pattern-recognition techniques for automating outlier exclusion during data processing, facilitating future adaptation to evolving experimental strategies. Full Article text
all Utilizing anomalous signals for element identification in macromolecular crystallography By journals.iucr.org Published On :: 2024-09-18 AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X-ray crystallography and cryo-electron microscopy, are often time-consuming and resource-intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post-translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X-ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f''. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions. Full Article text
all CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments By journals.iucr.org Published On :: 2024-10-01 A group of three deep-learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The first tool, a classification network, assigns images into categories relating to experimental outcomes. The other two tools are networks that perform both object detection and instance segmentation, resulting in masks of individual crystals in the first case and masks of crystallization droplets in addition to crystals in the second case, allowing the positions and sizes of these entities to be recorded. The creation of these tools used transfer learning, where weights from a pre-trained deep-learning network were used as a starting point and repurposed by further training on a relatively small set of data. Two of the tools are now integrated at the VMXi macromolecular crystallography beamline at DLS, where they have the potential to absolve the need for any user input, both for monitoring crystallization experiments and for triggering in situ data collections. The third is being integrated into the XChem fragment-based drug-discovery screening platform, also at DLS, to allow the automatic targeting of acoustic compound dispensing into crystallization droplets. Full Article text
all Analysis of crystallographic phase retrieval using iterative projection algorithms By journals.iucr.org Published On :: 2024-10-23 For protein crystals in which more than two thirds of the volume is occupied by solvent, the featureless nature of the solvent region often generates a constraint that is powerful enough to allow direct phasing of X-ray diffraction data. Practical implementation relies on the use of iterative projection algorithms with good global convergence properties to solve the difficult nonconvex phase-retrieval problem. In this paper, some aspects of phase retrieval using iterative projection algorithms are systematically explored, where the diffraction data and density-value distributions in the protein and solvent regions provide the sole constraints. The analysis is based on the addition of random error to the phases of previously determined protein crystal structures, followed by evaluation of the ability to recover the correct phase set as the distance from the solution increases. The properties of the difference-map (DM), relaxed–reflect–reflect (RRR) and relaxed averaged alternating reflectors (RAAR) algorithms are compared. All of these algorithms prove to be effective for crystallographic phase retrieval, and the useful ranges of the adjustable parameter which controls their behavior are established. When these algorithms converge to the solution, the algorithm trajectory becomes stationary; however, the density function continues to fluctuate significantly around its mean position. It is shown that averaging over the algorithm trajectory in the stationary region, following convergence, improves the density estimate, with this procedure outperforming previous approaches for phase or density refinement. Full Article text
all The role of alkyl chain length in the melt and solution crystallization of paliperidone aliphatic prodrugs By journals.iucr.org Published On :: 2024-01-01 Fatty acid-derivative prodrugs have been utilized extensively to improve the physicochemical, biopharmaceutical and pharmacokinetic properties of active pharmaceutical ingredients. However, to our knowledge, the crystallization behavior of prodrugs modified with different fatty acids has not been explored. In the present work, a series of paliperidone aliphatic prodrugs with alkyl chain lengths ranging from C4 to C16 was investigated with respect to crystal structure, crystal morphology and crystallization kinetics. The paliperidone derivatives exhibited isostructural crystal packing, despite the different alkyl chain lengths, and crystallized with the dominant (100) face in both melt and solution. The rate of crystallization for paliperidone derivatives in the melt increases with alkyl chain length owing to greater molecular mobility. In contrast, the longer chains prolong the nucleation induction time and reduce the crystal growth kinetics in solution. The results show a correlation between difficulty of nucleation in solution and the interfacial energy. This work provides insight into the crystallization behavior of paliperidone aliphatic prodrugs and reveals that the role of alkyl chain length in the crystallization behavior has a strong dependence on the crystallization method. Full Article text
all STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials By journals.iucr.org Published On :: 2024-01-01 Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25. Full Article text
all Orientational analysis of atomic pair correlations in nanocrystalline indium oxide thin films By journals.iucr.org Published On :: 2024-01-01 The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline In2O3-derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques. The atomic orientations of such films are known to vary based on the synthetic conditions. Here, an azimuthal orientational analysis of these films using GITXS with a single incident angle is shown to resolve the markedly different orientations of the atomic structures with respect to the planar support and the different degrees of long-range order, and hence, the terminal surface chemistries. It is anticipated that orientational analysis of GITXS/PDF data will offer opportunities to extend structural analyses of thin films by providing a means to qualitatively determine the major atomic orientation within nanocrystalline and, eventually, non-crystalline films. Full Article text
all The interoperability of crystallographic data and databases By journals.iucr.org Published On :: 2024-01-01 Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors. Driven by the success within these domains, the IUCr has worked closely with CODATA (the Committee on Data of the International Science Council) to help develop the latter's commitment to cross-domain integration of discipline-specific data. The IUCr has, in particular, emphasized the need for standards relating to data quality and completeness as an adjunct to the FAIR data landscape. This can ensure definitive reusable data, which in turn can aid interoperability across domains. A microsymposium at the IUCr 2023 Congress provided an up-to-date survey of data interoperability within and outside of crystallography, expounded using a broad range of examples. Full Article text
all Data reduction in protein serial crystallography By journals.iucr.org Published On :: 2024-02-08 Serial crystallography (SX) has become an established technique for protein structure determination, especially when dealing with small or radiation-sensitive crystals and investigating fast or irreversible protein dynamics. The advent of newly developed multi-megapixel X-ray area detectors, capable of capturing over 1000 images per second, has brought about substantial benefits. However, this advancement also entails a notable increase in the volume of collected data. Today, up to 2 PB of data per experiment could be easily obtained under efficient operating conditions. The combined costs associated with storing data from multiple experiments provide a compelling incentive to develop strategies that effectively reduce the amount of data stored on disk while maintaining the quality of scientific outcomes. Lossless data-compression methods are designed to preserve the information content of the data but often struggle to achieve a high compression ratio when applied to experimental data that contain noise. Conversely, lossy compression methods offer the potential to greatly reduce the data volume. Nonetheless, it is vital to thoroughly assess the impact of data quality and scientific outcomes when employing lossy compression, as it inherently involves discarding information. The evaluation of lossy compression effects on data requires proper data quality metrics. In our research, we assess various approaches for both lossless and lossy compression techniques applied to SX data, and equally importantly, we describe metrics suitable for evaluating SX data quality. Full Article text
all Droplet microfluidics for time-resolved serial crystallography By journals.iucr.org Published On :: 2024-03-01 Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis. A seeding strategy was used to overcome the improbability of Pdx1 nucleation occurring with diminishing droplet volumes. Convection within droplets was exploited for rapid crystal mixing with ligands. Mixing times of <2 ms were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be utilized to advance time-resolved serial crystallography. Full Article text
all KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography By journals.iucr.org Published On :: 2024-04-25 Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods. Full Article text
all Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development By journals.iucr.org Published On :: 2024-04-19 Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification. Full Article text
all RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures By journals.iucr.org Published On :: 2024-04-10 The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations. Full Article text
all The importance of definitions in crystallography By journals.iucr.org Published On :: 2024-05-28 This paper was motivated by the articles `Same or different – that is the question' in CrystEngComm (July 2020) and `Change to the definition of a crystal' in the IUCr Newsletter (June 2021). Experimental approaches to crystal comparisons require rigorously defined classifications in crystallography and beyond. Since crystal structures are determined in a rigid form, their strongest equivalence in practice is rigid motion, which is a composition of translations and rotations in 3D space. Conventional representations based on reduced cells and standardizations theoretically distinguish all periodic crystals. However, all cell-based representations are inherently discontinuous under almost any atomic displacement that can arbitrarily scale up a reduced cell. Hence, comparison of millions of known structures in materials databases requires continuous distance metrics. Full Article text
all The evolution of raw data archiving and the growth of its importance in crystallography By journals.iucr.org Published On :: 2024-06-12 The hardware for data archiving has expanded capacities for digital storage enormously in the past decade or more. The IUCr evaluated the costs and benefits of this within an official working group which advised that raw data archiving would allow ground truth reproducibility in published studies. Consultations of the IUCr's Commissions ensued via a newly constituted standing advisory committee, the Committee on Data. At all stages, the IUCr financed workshops to facilitate community discussions and possible methods of raw data archiving implementation. The recent launch of the IUCrData journal's Raw Data Letters is a milestone in the implementation of raw data archiving beyond the currently published studies: it includes diffraction patterns that have not been fully interpreted, if at all. The IUCr 75th Congress in Melbourne included a workshop on raw data reuse, discussing the successes and ongoing challenges of raw data reuse. This article charts the efforts of the IUCr to facilitate discussions and plans relating to raw data archiving and reuse within the various communities of crystallography, diffraction and scattering. Full Article text
all From X-ray crystallographic structure to intrinsic thermodynamics of protein–ligand binding using carbonic anhydrase isozymes as a model system By journals.iucr.org Published On :: 2024-06-10 Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein–ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure–thermodynamics correlations for the novel inhibitors of CA IX is discussed – an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein–Ligand Binding Database to understand general protein–ligand recognition principles that could be used in drug discovery. Full Article text
all Statistical optimization of guest uptake in crystalline sponges: grading structural outcomes By journals.iucr.org Published On :: 2024-06-12 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. Full Article text
all Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data By journals.iucr.org Published On :: 2024-07-10 Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile. Full Article text
all Bridging the microscopic divide: a comprehensive overview of micro-crystallization and in vivo crystallography By journals.iucr.org Published On :: 2024-06-27 A series of events underscoring the significant advancements in micro-crystallization and in vivo crystallography were held during the 26th IUCr Congress in Melbourne, positioning microcrystallography as a pivotal field within structural biology. Through collaborative discussions and the sharing of innovative methodologies, these sessions outlined frontier approaches in macromolecular crystallography. This review provides an overview of this rapidly moving field in light of the rich dialogues and forward-thinking proposals explored during the congress workshop and microsymposium. These advances in microcrystallography shed light on the potential to reshape current research paradigms and enhance our comprehension of biological mechanisms at the molecular scale. Full Article text
all Crystallographic phase identifier of a convolutional self-attention neural network (CPICANN) on powder diffraction patterns By journals.iucr.org Published On :: 2024-06-27 Spectroscopic data, particularly diffraction data, are essential for materials characterization due to their comprehensive crystallographic information. The current crystallographic phase identification, however, is very time consuming. To address this challenge, we have developed a real-time crystallographic phase identifier based on a convolutional self-attention neural network (CPICANN). Trained on 692 190 simulated powder X-ray diffraction (XRD) patterns from 23 073 distinct inorganic crystallographic information files, CPICANN demonstrates superior phase-identification power. Single-phase identification on simulated XRD patterns yields 98.5 and 87.5% accuracies with and without elemental information, respectively, outperforming JADE software (68.2 and 38.7%, respectively). Bi-phase identification on simulated XRD patterns achieves 84.2 and 51.5% accuracies, respectively. In experimental settings, CPICANN achieves an 80% identification accuracy, surpassing JADE software (61%). Integration of CPICANN into XRD refinement software will significantly advance the cutting-edge technology in XRD materials characterization. Full Article text
all Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography By journals.iucr.org Published On :: 2024-07-22 Light–oxygen–voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process. Full Article text
all In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry By journals.iucr.org Published On :: 2024-07-15 The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons. Full Article text
all Exploring serial crystallography for drug discovery By journals.iucr.org Published On :: 2024-07-29 Structure-based drug design is highly dependent on the availability of structures of the protein of interest in complex with lead compounds. Ideally, this information can be used to guide the chemical optimization of a compound into a pharmaceutical drug candidate. A limitation of the main structural method used today – conventional X-ray crystallography – is that it only provides structural information about the protein complex in its frozen state. Serial crystallography is a relatively new approach that offers the possibility to study protein structures at room temperature (RT). Here, we explore the use of serial crystallography to determine the structures of the pharmaceutical target, soluble epoxide hydrolase. We introduce a new method to screen for optimal microcrystallization conditions suitable for use in serial crystallography and present a number of RT ligand-bound structures of our target protein. From a comparison between the RT structural data and previously published cryo-temperature structures, we describe an example of a temperature-dependent difference in the ligand-binding mode and observe that flexible loops are better resolved at RT. Finally, we discuss the current limitations and potential future advances of serial crystallography for use within pharmaceutical drug discovery. Full Article text
all Bridging length scales in hard materials with ultra-small angle X-ray scattering – a critical review By journals.iucr.org Published On :: 2024-08-01 Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for in situ characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments. Full Article text
all Texture tomography, a versatile framework to study crystalline texture in 3D By journals.iucr.org Published On :: 2024-07-24 Crystallographic texture is a key organization feature of many technical and biological materials. In these materials, especially hierarchically structured ones, the preferential alignment of the nano constituents heavily influences the macroscopic behavior of the material. To study local crystallographic texture with both high spatial and angular resolution, we developed Texture Tomography (TexTOM). This approach allows the user to model the diffraction data of polycrystalline materials using the full reciprocal space of the crystal ensemble and describe the texture in each voxel via an orientation distribution function, hence it provides 3D reconstructions of the local texture by measuring the probabilities of all crystal orientations. The TexTOM approach addresses limitations associated with existing models: it correlates the intensities from several Bragg reflections, thus reducing ambiguities resulting from symmetry. Further, it yields quantitative probability distributions of local real space crystal orientations without further assumptions about the sample structure. Finally, its efficient mathematical formulation enables reconstructions faster than the time scale of the experiment. This manuscript presents the mathematical model, the inversion strategy and its current experimental implementation. We show characterizations of simulated data as well as experimental data obtained from a synthetic, inorganic model sample: the silica–witherite biomorph. TexTOM provides a versatile framework to reconstruct 3D quantitative texture information for polycrystalline samples; it opens the door for unprecedented insights into the nanostructural makeup of natural and technical materials. Full Article text
all Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography By journals.iucr.org Published On :: 2024-10-29 OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates. Full Article text
all High-throughput nanoscale crystallization of dihydropyridine active pharmaceutical ingredients By journals.iucr.org Published On :: 2023-12-21 Single-crystal X-ray diffraction analysis of small molecule active pharmaceutical ingredients is a key technique in the confirmation of molecular connectivity, including absolute stereochemistry, as well as the solid-state form. However, accessing single crystals suitable for X-ray diffraction analysis of an active pharmaceutical ingredient can be experimentally laborious, especially considering the potential for multiple solid-state forms (solvates, hydrates and polymorphs). In recent years, methods for the exploration of experimental crystallization space of small molecules have undergone a `step-change', resulting in new high-throughput techniques becoming available. Here, the application of high-throughput encapsulated nanodroplet crystallization to a series of six dihydropyridines, calcium channel blockers used in the treatment of hypertension related diseases, is described. This approach allowed 288 individual crystallization experiments to be performed in parallel on each molecule, resulting in rapid access to crystals and subsequent crystal structures for all six dihydropyridines, as well as revealing a new solvate polymorph of nifedipine (1,4-dioxane solvate) and the first known solvate of nimodipine (DMSO solvate). This work further demonstrates the power of modern high-throughput crystallization methods in the exploration of the solid-state landscape of active pharmaceutical ingredients to facilitate crystal form discovery and structural analysis by single-crystal X-ray diffraction. Full Article text
all Current developments and trends in quantum crystallography By journals.iucr.org Published On :: 2024-06-18 Quantum crystallography is an emerging research field of science that has its origin in the early days of quantum physics and modern crystallography when it was almost immediately envisaged that X-ray radiation could be somehow exploited to determine the electron distribution of atoms and molecules. Today it can be seen as a composite research area at the intersection of crystallography, quantum chemistry, solid-state physics, applied mathematics and computer science, with the goal of investigating quantum problems, phenomena and features of the crystalline state. In this article, the state-of-the-art of quantum crystallography will be described by presenting developments and applications of novel techniques that have been introduced in the last 15 years. The focus will be on advances in the framework of multipole model strategies, wavefunction-/density matrix-based approaches and quantum chemical topological techniques. Finally, possible future improvements and expansions in the field will be discussed, also considering new emerging experimental and computational technologies. Full Article text
all Determining magnetic structures in GSAS-II using the Bilbao Crystallographic Server tool k-SUBGROUPSMAG By journals.iucr.org Published On :: 2024-09-20 The embedded call to a special version of the web-based Bilbao Crystallographic Server tool k-SUBGROUPSMAG from within GSAS-II to form a list of all possible commensurate magnetic subgroups of a parent magnetic grey group is described. It facilitates the selection and refinement of the best commensurate magnetic structure model by having all the analysis tools including Rietveld refinement in one place as part of GSAS-II. It also provides the chosen magnetic space group as one of the 1421 possible standard Belov–Neronova–Smirnova forms or equivalent non-standard versions. Full Article text
all Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1 By journals.iucr.org Published On :: 2024-11-06 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. Full Article text
all Synthesis and crystallographic characterization of 6-hydroxy-1,2-dihydropyridin-2-one By journals.iucr.org Published On :: 2023-11-14 The title compound, C5H5NO2, is a hydroxylated pyridine ring that has been studied for its involvement in microbial degradation of nicotinic acid. Here we describe its synthesis as a formic acid salt, rather than the standard hydrochloride salt that is commercially available, and its spectroscopic and crystallographic characterization. Full Article text
all Synthesis, crystal structure and Hirshfeld analysis of trans-bis(2-{1-[(6R,S)-3,5,5,6,8,8-hexamethyl-5,6,7,8-tetrahydronaphthalen-2-yl]ethylidene}-N-methylhydrazinecarbothioamidato-κ2N2,S)palladium(II) ethanol mon By journals.iucr.org Published On :: 2023-11-16 The reaction between the (R,S)-fixolide 4-methylthiosemicarbazone and PdII chloride yielded the title compound, [Pd(C20H30N3S)2]·C2H6O {common name: trans-bis[(R,S)-fixolide 4-methylthiosemicarbazonato-κ2N2S]palladium(II) ethanol monosolvate}. The asymmetric unit of the title compound consists of one bis-thiosemicarbazonato PdII complex and one ethanol solvent molecule. The thiosemicarbazononato ligands act as metal chelators with a trans configuration in a distorted square-planar geometry. A C—H⋯S intramolecular interaction, with graph-set motif S(6), is observed and the coordination sphere resembles a hydrogen-bonded macrocyclic environment. Additionally, one C—H⋯Pd anagostic interaction can be suggested. Each ligand is disordered over the aliphatic ring, which adopts a half-chair conformation, and two methyl groups [s.o.f. = 0.624 (2):0.376 (2)]. The disorder includes the chiral carbon atoms and, remarkably, one ligand has the (R)-isomer with the highest s.o.f. value atoms, while the other one shows the opposite, the atoms with the highest s.o.f. value are associated with the (S)-isomer. The N—N—C(=S)—N fragments of the ligands are approximately planar, with the maximum deviations from the mean plane through the selected atoms being 0.0567 (1) and −0.0307 (8) Å (r.m.s.d. = 0.0403 and 0.0269 Å) and the dihedral angle with the respective aromatic rings amount to 46.68 (5) and 50.66 (4)°. In the crystal, the complexes are linked via pairs of N—H⋯S interactions, with graph-set motif R22(8), into centrosymmetric dimers. The dimers are further connected by centrosymmetric pairs of ethanol molecules, building mono-periodic hydrogen-bonded ribbons along [011]. The Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are [atoms with highest/lowest s.o.f.s considered separately]: H⋯H (81.6/82.0%), H⋯C/C⋯H (6.5/6.4%), H⋯N/N⋯H (5.2/5.0%) and H⋯S/S⋯H (5.0/4.9%). Full Article text
all When a dream comes true: birth of the African Crystallographic Association (AfCA) By journals.iucr.org Published On :: 2024-01-05 This paper summarizes brief perspectives on the historic process of establishing an African Crystallographic Association (AfCA) and includes representative references. It covers activities within four arbitrarily selected, approximate time slots, i.e., 1890s–1999, 2000–2013, 2014–2019 and 2020–2023. A genuine attempt is made to include appropriate role players, organizations and accompanying events within these periods. It concludes with the official admission of AfCA as the fifth Regional Associate of the IUCr at the 26th Congress and General Assembly of the IUCr in Melbourne, Australia in 2023. Full Article text
all (S)-(+)-1-(4-Bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine and bis{(S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine-κN}dichloridopalladium(II) By journals.iucr.org Published On :: 2024-01-26 The (S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine ligand, C16H16BrNO, (I), was synthesized through the reaction of 4-methoxyanisaldehyde with (S)-(−)-1-(4-bromophenyl)ethylamine. It crystallizes in the orthorhombic space group P212121 belonging to the Sohncke group, featuring a single molecule in the asymmetric unit. The refinement converged successfully, achieving an R factor of 0.0508. The PdII complex bis{(S)-(+)-1-(4-bromophenyl)-N-[(4-methoxyphenyl)methylidene]ethylamine-κN}dichloridopalladium(II), [PdCl2(C16H16BrNO)2], (II), crystallizes in the monoclinic space group P21 belonging to the Sohncke group, with two molecules in the asymmetric unit. The central atom is tetracoordinated by two N atoms and two Cl atoms, resulting in a square-planar configuration. The imine moieties exhibit a trans configuration around the PdII centre, with average Cl—Pd—N angles of approximately 89.95 and 90°. The average distances within the palladium complex for the two molecules are ∼2.031 Å for Pd—N and ∼2.309 Å for Pd—Cl. Full Article text
all Cadmium phosphates Cd2(PO4)OH and Cd5(PO4)2(OH)4 crystallizing in mineral structures By journals.iucr.org Published On :: 2024-01-26 Single crystals of two basic cadmium phosphates, dicadmium orthophosphate hydroxide, Cd2(PO4)OH, and pentacadmium bis(orthophosphate) tetrakis(hydroxide), Cd5(PO4)2(OH)4, were obtained under hydrothermal conditions. Cd2(PO4)OH adopts the triplite [(Mn,Fe)2(PO4)F] structure type. Its asymmetric unit comprises two Cd, one P and five O sites, all situated at the general Wyckoff position 8 f of space group I2/a; two of the O atoms are positionally disordered over two sites, and the H atom could not be localized. Disregarding the disorder, distorted [CdO6] polyhedra form a tri-periodic network by edge-sharing with neighbouring [CdO6] units and by vertex-sharing with [PO4] units. The site associated with the OH group is coordinated by four Cd atoms in a distorted tetrahedral manner forming 1∞[(OH)Cd4/2] chains parallel to [001]. The oxygen environment around the OH site suggests multiple acceptor atoms for possible O—H⋯O hydrogen-bonding interactions and is the putative reason for the disorder. Cd5(PO4)2(OH)4 adopts the arsenoclasite [Mn5(AsO4)2(OH)4] structure type. Its asymmetric unit comprises five Cd, two P, and twelve O sites all located at the general Wyckoff position 4 a of space group P212121; the H atoms could not be localized. The crystal structure of Cd5(PO4)2(OH)4 can be subdivided into two main sub-units. One consists of three edge-sharing [CdO6] octahedra, and the other of two edge- and vertex-sharing [CdO6] octahedra. Each sub-unit forms corrugated ribbons extending parallel to [100]. The two types of ribbons are linked into the tri-periodic arrangement through vertex-sharing and through common [PO4] tetrahedra. Quantitative structure comparisons are made with isotypic M5(XO4)2(OH)4 crystal structures (M = Cd, Mn, Co; X = P, As, V). Full Article text
all Structural characterization of a new samarium–sodium heterometallic coordination polymer By journals.iucr.org Published On :: 2024-02-06 Lanthanide-containing materials are of interest in the field of crystal engineering because of their unique properties and distinct structure types. In this context, a new samarium–sodium heterometallic coordination polymer, poly[tetrakis(μ2-2-formyl-6-methoxyphenolato)samarium(III)sodium(I)], {[SmNa(C8H7O3)4]·solvent}n (Sm-1), was synthesized and crystallized via slow evaporation from a mixture of ethanol and acetonitrile. The compound features alternating SmIII and NaI ions, which are linked by ortho-vanillin (o-vanillin) ligands to form a mono-periodic chain-like coordination polymer. The chains propagate along the [001] direction. Residual electron density of disordered solvent molecules in the void space could not be reasonably modeled, thus the SQUEEZE function was applied. The structural, vibrational, and optical properties are reported. Full Article text
all ‘Young crystallographers’ rejuvenate crystallography in Germany By journals.iucr.org Published On :: 2024-02-27 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. Full Article text
all The unanticipated oxidation of a tertiary amine in a tetracyclic glyoxal-cyclam condensate yielding zinc(II) coordinated to a sterically hindered amine oxide By journals.iucr.org Published On :: 2024-03-06 The complex, trichlorido(1,4,11-triaza-8-azoniatetracyclo[6.6.2.04,16.011,15]hexadecane 1-oxide-κO)zinc(II) monohydrate, [ZnCl3(C12H23N4O)]·H2O, (I), has monoclinic symmetry (space group P21/n) at 120 K. The zinc(II) center adopts a slightly distorted tetrahedral coordination geometry and is coordinated by three chlorine atoms and the oxygen atom of the oxidized tertiary amine of the tetracycle. The amine nitrogen atom, inside the ligand cleft, is protonated and forms a hydrogen bond to the oxygen of the amine oxide. Additional hydrogen-bonding interactions involve the protonated amine, the water solvate oxygen atom, and one of the chloro ligands. Full Article text
all Crystal structure of bis{2-[5-(3,4,5-trimethoxyphenyl)-4H-1,2,4-triazol-3-yl]pyridine}palladium(II) bis(trifluoroacetate) trifluoroacetic acid disolvate By journals.iucr.org Published On :: 2024-05-03 The new palladium(II) complex, [Pd(C16H16N4O3)2](CF3COO)2·2CF3COOH, crystallizes in the triclinic space group Poverline{1} with the asymmetric unit containing half the cation (PdII site symmetry Ci), one trifluoroactetate anion and one co-crystallized trifluoroacetic acid molecule. Two neutral chelating 2-[5-(3,4,5-trimethoxyphenyl)-4H-1,2,4-triazol-3-yl]pyridine ligands coordinate to the PdII ion through the triazole-N and pyridine-N atoms in a distorted trans-PdN4 square-planar configuration [Pd—N 1.991 (2), 2.037 (2) Å; cis N—Pd—N 79.65 (8), 100.35 (8)°]. The complex cation is quite planar, except for the methoxo groups (δ = 0.117 Å for one of the C atoms). The planar configuration is supported by two intramolecular C—H⋯N hydrogen bonds. In the crystal, the π–π-stacked cations are arranged in sheets parallel to the ab plane that are flanked on both sides by the trifluoroacetic acid–trifluoroacetate anion pairs. Apart from classical N/O—H⋯O hydrogen-bonding interactions, weak C—H⋯F/N/O contacts consolidate the three-dimensional architecture. Both trifluoroacetic moieties were found to be disordered over two resolvable positions with a refined occupancy ratio of 0.587 (1):0.413 (17) and 0.530 (6):0.470 (6) for the protonated and deprotonated forms, respectively. Full Article text
all Crystal structure of hexachlorothallate within a caesium chloride–phosphotungstate lattice Cs9(TlCl6)(PW12O40)2·9CsCl By journals.iucr.org Published On :: 2024-06-14 Crystal formation of caesium thallium chloride phosphotungstates, Cs9(TlCl6)(PW12O40)2·9CsCl showcases the ability to capture and crystallize octahedral complexes via the use of polyoxometalates (POMs). The large number of caesium chlorides allows for the POM [α-PW12O40]3− to arrange itself in a cubic close-packing lattice extended framework, in which the voids created enable the capture of the [TlCl6]3− complex. Full Article text
all Crystal structure and Hirshfeld surface analysis of a halogen bond between 2-(allylthio)pyridine and 1,2,4,5-tetrafluoro-3,6-diiodobenzene By journals.iucr.org Published On :: 2024-06-21 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%. Full Article text
all Synthesis, crystal structure and thermal properties of catena-poly[[bis(4-methylpyridine)nickel(II)]-di-μ-thiocyanato], which shows an alternating all-trans and cis–cis–trans-coordination of the NiS2Np2Nt2 octahedra (p = 4-me By journals.iucr.org Published On :: 2024-06-21 The title compound, [Ni(NCS)2(C6H7N)2]n, was prepared by the reaction of Ni(NCS)2 with 4-methylpyridine in water. Its asymmetric unit consists of two crystallographically independent NiII cations, of which one is located on a twofold rotational axis whereas the second occupies a center of inversion, two independent thiocyanate anions and two independent 4-methylpyridine coligands in general positions. Each NiII cation is octahedrally coordinated by two 4-methylpyridine coligands as well as two N- and two S-bonded thiocyanate anions. One of the cations shows an all-trans, the other a cis–cis–trans configuration. The metal centers are linked by pairs of μ-1,3-bridging thiocyanate anions into [101] chains. X-ray powder diffraction shows that a pure crystalline phase has been obtained and thermogravimetry coupled to differential thermoanalysis reveals that the title compound loses half of the 4-methylpyridine coligands and transforms into Ni(NCS)2(C6H7N). Nearly pure samples of this compound can be obtained by thermal annealing and a Rietveld refinement demonstrated that it is isotypic to its recently reported Cd analog [Neumann et al., (2020). CrystEngComm. 22, 184–194] In its crystal structure, the metal cations are linked by one μ-1,3(N,S)- and one μ-1,3,3(N,S,S)-bridging thiocyanate anion into single chains that condense via the μ-1,3,3(N,S,S)-bridging anionic ligands into double chains. Full Article text
all Pyrazine-bridged polymetallic copper–iridium clusters By journals.iucr.org Published On :: 2024-07-27 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). Full Article text