IUCrJ最新文献

{"title":"Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors","authors":"Michał Chodkiewicz ,&nbsp;Leonid Patrikeev ,&nbsp;Sylwia Pawlędzio ,&nbsp;Krzysztof Woźniak ,&nbsp;P. Lightfoot (Editor)","doi":"10.1107/S2052252524001507","DOIUrl":"10.1107/S2052252524001507","url":null,"abstract":"<div><p>A databank of atomic densities calculated using Hirshfeld partition has been developed which allows for refinement with similar accuracy to Hirshfeld atom refinement without the need for time-consuming wavefunction calculations.</p></div><div><p>Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to <em>l</em> = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 249-259"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae","authors":"Badri S. Rajagopal ,&nbsp;Nick Yates ,&nbsp;Jake Smith ,&nbsp;Alessandro Paradisi ,&nbsp;Catherine Tétard-Jones ,&nbsp;William G. T. Willats ,&nbsp;Susan Marcus ,&nbsp;J. Paul Knox ,&nbsp;Mohd Firdaus-Raih ,&nbsp;Bernard Henrissat ,&nbsp;Gideon J. Davies ,&nbsp;Paul H. Walton ,&nbsp;Alison Parkin ,&nbsp;Glyn R. Hemsworth ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S2052252524001386","DOIUrl":"10.1107/S2052252524001386","url":null,"abstract":"<div><p>The structures of novel redox domains extracted from two large extracellular redox proteins encoded in the genome of <em>Teredinibacter turnerae</em> suggest potentially novel roles for electron-transfer proteins in carbohydrate chemistry outside of the cell.</p></div><div><p>The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about polysaccharide oxidation. In bacteria, less is known about the interplay between redox proteins and LPMOs, or how the interaction between the two contributes to polysaccharide degradation. We therefore set out to characterize two previously unstudied proteins from the shipworm symbiont <em>Teredinibacter turnerae</em> that were initially identified by the presence of carbohydrate binding domains appended to uncharacterized domains with probable redox functions. Here, X-ray crystal structures of several domains from these proteins are presented together with initial efforts to characterize their functions. The analysis suggests that the target proteins are unlikely to function as LPMO electron donors, raising new questions as to the potential redox functions that these large extracellular multi-haem-containing <em>c</em>-type cytochromes may perform in these bacteria.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 260-274"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Droplet microfluidics for time-resolved serial crystallography","authors":"Jack Stubbs ,&nbsp;Theo Hornsey ,&nbsp;Niall Hanrahan ,&nbsp;Luis Blay Esteban ,&nbsp;Rachel Bolton ,&nbsp;Martin Malý ,&nbsp;Shibom Basu ,&nbsp;Julien Orlans ,&nbsp;Daniele de Sanctis ,&nbsp;Jung-uk Shim ,&nbsp;Patrick D. Shaw Stewart ,&nbsp;Allen M. Orville ,&nbsp;Ivo Tews ,&nbsp;Jonathan West ,&nbsp;F. Maia (Editor)","doi":"10.1107/S2052252524001799","DOIUrl":"10.1107/S2052252524001799","url":null,"abstract":"<div><p>Microfluidic manipulation of droplet volume coupled with seeding can be used to precisely control crystal size. Droplet microfluidics also enables fast, millisecond-scale micromixing for advancing time-resolved serial crystallography.</p></div><div><p>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 <em>Arabidopsis</em> 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 &lt;2 ms were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be utilized to advance time-resolved serial crystallography.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 237-248"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Data reduction in protein serial crystallography","authors":"Marina Galchenkova ,&nbsp;Alexandra Tolstikova ,&nbsp;Bjarne Klopprogge ,&nbsp;Janina Sprenger ,&nbsp;Dominik Oberthuer ,&nbsp;Wolfgang Brehm ,&nbsp;Thomas A. White ,&nbsp;Anton Barty ,&nbsp;Henry N. Chapman ,&nbsp;Oleksandr Yefanov ,&nbsp;G. Williams (Editor)","doi":"10.1107/S205225252400054X","DOIUrl":"10.1107/S205225252400054X","url":null,"abstract":"<div><p>Various approaches for lossless and lossy compression are evaluated, and suitable quality assessment metrics for serial crystallographic data – used in combination with lossy data reduction – are described.</p></div><div><p>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.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 190-201"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139702580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the components of diffuse scattering using deep learning","authors":"Chloe A. Fuller ,&nbsp;Lucas S. P. Rudden ,&nbsp;V. T. Forsyth (Editor)","doi":"10.1107/S2052252523009521","DOIUrl":"10.1107/S2052252523009521","url":null,"abstract":"<div><p>A deep-learning method is applied to separate the components of diffuse scattering from chemical short-range order and the molecular form factor. The method is validated against a large simulated dataset and further tested on a real example, resulting in output components of sufficient quality to use for quantitative analysis.</p></div><div><p>Many technologically important material properties are underpinned by disorder and short-range structural correlations; therefore, elucidating structure–property relationships in functional materials requires understanding both the average and the local structures. The latter information is contained within diffuse scattering but is challenging to exploit, particularly in single-crystal systems. Separation of the diffuse scattering into its constituent components can greatly simplify analysis and allows for quantitative parameters describing the disorder to be extracted directly. Here, a deep-learning method, DSFU-Net, is presented based on the Pix2Pix generative adversarial network, which takes a plane of diffuse scattering as input and factorizes it into the contributions from the molecular form factor and the chemical short-range order. DSFU-Net was trained on 198 421 samples of simulated diffuse scattering data and performed extremely well on the unseen simulated validation dataset in this work. On a real experimental example, DSFU-Net successfully reproduced the two components with a quality sufficient to distinguish between similar structural models based on the form factor and to refine short-range-order parameters, achieving values comparable to other established methods. This new approach could streamline the analysis of diffuse scattering as it requires minimal prior knowledge of the system, allows access to both components in seconds and is able to compensate for small regions with missing data. DSFU-Net is freely available for use and represents a first step towards an automated workflow for the analysis of single-crystal diffuse scattering.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 1","pages":"Pages 34-44"},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92154361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"C-SPAM: an open-source time-resolved specimen vitrification device with light-activated molecules","authors":"Alejandra Montaño Romero ,&nbsp;Calli Bonin ,&nbsp;Edward C. Twomey ,&nbsp;F. Sun (Editor)","doi":"10.1107/S2052252523010308","DOIUrl":"10.1107/S2052252523010308","url":null,"abstract":"<div><p>An open-source platform for light-coupled cryo-electron microscopy specimen preparation is presented.</p></div><div><p>Molecular structures can be determined <em>in vitro</em> and <em>in situ</em> with cryo-electron microscopy (cryo-EM). Specimen preparation is a major obstacle in cryo-EM. Typical sample preparation is orders of magnitude slower than biological processes. Time-resolved cryo-EM (TR-cryo-EM) can capture short-lived states. Here, Cryo-EM sample preparation with light-activated molecules (C-SPAM) is presented, an open-source, photochemistry-coupled device for TR-cryo-EM that enables millisecond resolution and tunable timescales across broad biological applications.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 1","pages":"Pages 16-22"},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138804098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval based on deep learning","authors":"Fucheng Yu ,&nbsp;Kang Du ,&nbsp;Xiaolu Ju ,&nbsp;Feixiang Wang ,&nbsp;Ke Li ,&nbsp;Can Chen ,&nbsp;Guohao Du ,&nbsp;Biao Deng ,&nbsp;Honglan Xie ,&nbsp;Tiqiao Xiao ,&nbsp;M. Takata (Editor)","doi":"10.1107/S2052252523010114","DOIUrl":"10.1107/S2052252523010114","url":null,"abstract":"<div><p>A deep-learning based speckle-tracking imaging method is developed, and high-accuracy phase retrieval is successfully achieved with a single shot.</p></div><div><p>Speckle-tracking X-ray imaging is an attractive candidate for dynamic X-ray imaging owing to its flexible setup and simultaneous yields of phase, transmission and scattering images. However, traditional speckle-tracking imaging methods suffer from phase distortion at locations with abrupt changes in density, which is always the case for real samples, limiting the applications of the speckle-tracking X-ray imaging method. In this paper, we report a deep-learning based method which can achieve dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval. The calibration results of a phantom show that the profile of the retrieved phase is highly consistent with the theoretical one. Experiments of polyurethane foaming demonstrated that the proposed method revealed the evolution of the complicated microstructure of the bubbles accurately. The proposed method is a promising solution for dynamic X-ray imaging with high-accuracy phase retrieval, and has extensive applications in metrology and quantitative analysis of dynamics in material science, physics, chemistry and biomedicine.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 1","pages":"Pages 73-81"},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138804100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new era is emerging at scientific user facilities.","authors":"Dimitri Argyriou","doi":"10.1107/S2052252523010928","DOIUrl":"10.1107/S2052252523010928","url":null,"abstract":"<p><p>Global scientific exchange has been profoundly perturbed by the COVID-19 pandemic, altering user travel behaviours and accelerating the use of remote access. Combined with the advent of artificial intelligence (AI), these trends together can change how large-scale user scientific facilities are used by the community and managed by operators.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"1-2"},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138829825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The interoperability of crystallographic data and databases","authors":"Alice Brink ,&nbsp;Ian Bruno ,&nbsp;John R. Helliwell ,&nbsp;Brian McMahon ,&nbsp;P. Lightfoot (Editor)","doi":"10.1107/S2052252523010424","DOIUrl":"10.1107/S2052252523010424","url":null,"abstract":"<div><p>Interoperability of scientific data within crystallography has been achieved to a high level by the adoption of standard exchange formats and protocols. Extending such interoperability across other disciplines is a goal of the International Science Council Committee CODATA, to which the IUCr has been a leading contributor. Our article combines a description of the importance of interoperability for addressing grand challenges with a desire to stimulate the crystallographic community to continue exploring this topic.</p></div><div><p>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.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 1","pages":"Pages 9-15"},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138829827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of alkyl chain length in the melt and solution crystallization of paliperidone aliphatic prodrugs","authors":"An Chen ,&nbsp;Peishan Cai ,&nbsp;Yayun Peng ,&nbsp;Minshan Guo ,&nbsp;Yuan Su ,&nbsp;Ting Cai ,&nbsp;L. R. MacGillivray (Editor)","doi":"10.1107/S2052252523009582","DOIUrl":"10.1107/S2052252523009582","url":null,"abstract":"<div><p>Structural determination and crystallization behavior of paliperidone prodrugs modified with different alkyl chain lengths is described.</p></div><div><p>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.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 1","pages":"Pages 23-33"},"PeriodicalIF":3.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92154360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}