IUCrJ最新文献

{"title":"The use of machine learning interatomic potentials for the verification of experimental molecular crystal structures","authors":"M. Hušák, F. Fňukal, J. Čejka","doi":"10.1107/S2052252526006949","DOIUrl":"10.1107/S2052252526006949","url":null,"abstract":"<div><div>A correctly solved crystal structure should agree with the experimental data, and its geometry should correspond to a local minimum on the potential energy surface (PES). The idea of verifying crystal structure solutions by comparing them with their geometry-optimized versions was introduced 15 years ago. Recent developments in machine learning interatomic potentials (MLIPs) have made it possible to replace computationally expensive density functional theory (DFT) calculations with AI/neural-network-based alternatives. MLIPs can reach DFT-comparable precision with a substantial gain in speed. We selected one promising MLIP, Universal Models for Atoms, trained on the Open Molecular Crystals 2025 dataset, and processed a prefiltered subset of 216 919 structures from the Cambridge Structural Database. Due to the limitations of the MLIP available when this study commenced, ionic compounds, salts and metal-containing structures were excluded. The current methodology cannot process disordered structures, and available computational resources limit the maximum unit-cell volume that can be treated to 4000 Å<sup>3</sup>. All structures in the dataset were geometry optimized using the MLIP, and similarity descriptors were calculated to quantify the differences between the original and optimized structures. Automatic analysis was followed by the manual identification of issues indicated by the descriptors’ values. We detected anomalies in experimental structures that had already passed all prior validation, as well as limitations in the reliability of the MLIP PES calculations. For 1867 crystal structures, bond-pattern change was observed, while 3331 structures showed a root-mean-square Cartesian displacement greater than 0.25 Å. Future improvements to the methodology and extension to systems not covered by this study are discussed.</div></div><div>A correctly solved crystal structure should agree with the experimental data, and its geometry should correspond to a local minimum on the potential energy surface (PES). The idea of verifying crystal structure solutions by comparing them with their geometry-optimized versions was introduced 15 years ago. Recent developments in machine learning interatomic potentials (MLIPs) have made it possible to replace computationally expensive density functional theory (DFT) calculations with AI/neural-network-based alternatives. MLIPs can reach DFT-comparable precision with a substantial gain in speed. We selected one promising MLIP, Universal Models for Atoms, trained on the Open Molecular Crystals 2025 dataset, and processed a prefiltered subset of 216 919 structures from the Cambridge Structural Database. Due to the limitations of the MLIP available when this study commenced, ionic compounds, salts and metal-containing structures were excluded. The current methodology cannot process disordered structures, and available computational resources limit the maximum unit-cell volume that can be treated to 4000 Å<sup","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 623-634"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148591678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Post-acquisition super resolution for cryo-electron microscopy","authors":"Raymond N. Burton Smith,&nbsp;Kazuyoshi Murata","doi":"10.1107/S2052252526005348","DOIUrl":"10.1107/S2052252526005348","url":null,"abstract":"<div><div>Recently, reports have demonstrated achieving resolutions beyond the physical Nyquist limit using super resolution acquisition. Here, we demonstrate exceeding this limitation by pre-processing the raw micrograph movies from counting mode data that have already reached the physical Nyquist reconstruction resolution. To demonstrate functionality, micrograph movies of multiple datasets were pre-processed, showing that it is possible to exceed the physical Nyquist limit via pixel doubling before motion correction. We call this ‘post-acquisition super resolution’, or PASR. While this was originally developed for processing of giant virus datasets, where acquiring at high magnification is not always possible or desirable, it is also shown to work for smaller objects such as adeno-associated virus and apoferritin, both of which are high symmetry, and jack bean urease, with lower symmetry. PASR reduces the magnification required to achieve desired resolutions, which may increase collection efficiency. Further, PASR may be applied on top of acquisition-time super resolution data collection, allowing results to exceed not just the physical sampling limit, but also the super resolution sampling limit. However, to benefit from PASR, data must already reach the Nyquist limit.</div></div><div>Recently, reports have demonstrated achieving resolutions beyond the physical Nyquist limit using super resolution acquisition. Here, we demonstrate exceeding this limitation by pre-processing the raw micrograph movies from counting mode data that have already reached the physical Nyquist reconstruction resolution. To demonstrate functionality, micrograph movies of multiple datasets were pre-processed, showing that it is possible to exceed the physical Nyquist limit via pixel doubling before motion correction. We call this ‘post-acquisition super resolution’, or PASR. While this was originally developed for processing of giant virus datasets, where acquiring at high magnification is not always possible or desirable, it is also shown to work for smaller objects such as adeno-associated virus and apoferritin, both of which are high symmetry, and jack bean urease, with lower symmetry. PASR reduces the magnification required to achieve desired resolutions, which may increase collection efficiency. Further, PASR may be applied on top of acquisition-time super resolution data collection, allowing results to exceed not just the physical sampling limit, but also the super resolution sampling limit. However, to benefit from PASR, data must already reach the Nyquist limit.</div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 589-605"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148874101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Considerations for FAIR data catalogs from DAPHNE4NFDI","authors":"Bishoy Hakim,&nbsp;Fabio Dall’Antonia,&nbsp;Johannes Dallmann,&nbsp;Christian Felder,&nbsp;Abhijeet Gaur,&nbsp;Heike Görzig,&nbsp;Nicolas Hayen,&nbsp;Regina Hinzmann,&nbsp;Julia Kobus,&nbsp;Rolf Krahl,&nbsp;Bridget Murphy,&nbsp;Sebastian Paripsa,&nbsp;Björn Pedersen,&nbsp;Agha Raza,&nbsp;Kristin Tippey,&nbsp;Tim Wetzel,&nbsp;Alexander Zaft,&nbsp;Tobias Unruh,&nbsp;Sebastian Busch","doi":"10.1107/S2052252526006871","DOIUrl":"10.1107/S2052252526006871","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Large-scale photon and neutron (PaN) experiments generate vast amounts of valuable data, yet implementation of the FAIR principles (findable, accessible, interoperable and reusable) remains incomplete. Metadata catalogs are a key tool for addressing this challenge. They do not store data itself but provide structured searchable descriptions that make datasets discoverable and reusable. This article, developed within the DAPHNE4NFDI consortium of Germany’s National Research Data Infrastructure (NFDI), reflects the discussion on the role of metadata catalogs in PaN science such as SciCat, ICAT and SampleDB from a scientific point of view, and presents the status of current implementations. Integration of standards such as NeXus, sample databases and electronic laboratory notebooks is also addressed. Catalog implementations are categorized by purpose as raw data, institutional data and public data, and examined by practical aspects including authentication and authorization, persistent identifiers, and metadata enrichment. Drawing on case studies such as the RefXAS X-ray absorption spectroscopy database, we summarize lessons learned and present recommendations for minimizing fragmentation, enabling interoperability, and harmonizing identity and persistent-identifier policies. Looking ahead, semantic technologies and knowledge graphs will play a central role in building a federated FAIR-compliant catalog infrastructure that supports both facility and university researchers.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;Large-scale photon and neutron (PaN) experiments generate vast amounts of valuable data, yet implementation of the FAIR principles (findable, accessible, interoperable and reusable) remains incomplete. Metadata catalogs are a key tool for addressing this challenge. They do not store data itself but provide structured searchable descriptions that make datasets discoverable and reusable. This article, developed within the DAPHNE4NFDI consortium of Germany’s National Research Data Infrastructure (NFDI), reflects the discussion on the role of metadata catalogs in PaN science such as SciCat, ICAT and SampleDB from a scientific point of view, and presents the status of current implementations. Integration of standards such as NeXus, sample databases and electronic laboratory notebooks is also addressed. Catalog implementations are categorized by purpose as raw data, institutional data and public data, and examined by practical aspects including authentication and authorization, persistent identifiers, and metadata enrichment. Drawing on case studies such as the RefXAS X-ray absorption spectroscopy database, we summarize lessons learned and present recommendations for minimizing fragmentation, enabling interoperability, and harmonizing identity and persistent-identifier policies. Looking ahead, semantic technologies and knowledge graphs will play a central role in building a federated FAIR-compliant catalog infrastructure that supports both facility and universi","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 541-551"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148684614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Droplet-on-demand tape drive and X-ray emission spectroscopy prototypes for time-resolved serial crystallography on VMXi at Diamond Light Source","authors":"Pierre Aller,&nbsp;Juan Sanchez-Weatherby,&nbsp;Abbey Telfer,&nbsp;Robert Bosman,&nbsp;Nicholas Devenish,&nbsp;Philip Hinchliffe,&nbsp;Sam Horrell,&nbsp;Jophy Ip,&nbsp;Richard Littlewood,&nbsp;Andrew Male,&nbsp;Eva Gimenez Navarro,&nbsp;Urszula Neuman,&nbsp;Jos J. A. G. Kamps,&nbsp;David Omar,&nbsp;Laura Parkinson,&nbsp;Muthraj Pandi,&nbsp;Nico Rubies,&nbsp;James Sandy,&nbsp;Anastasya Shilova,&nbsp;James Spencer,&nbsp;Allen M. Orville","doi":"10.1107/S2052252526005658","DOIUrl":"10.1107/S2052252526005658","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Time-resolved X-ray crystallography is experiencing a resurgence, in part because of serial methods that readily allow scientists to create stop-motion movies of the macromolecular functions of photoactivation, enzyme-catalysed reactions and ligand-induced conformational changes triggering further downstream signalling events. While some reactions can be initiated with light, either naturally or using photocaged compounds, a more generally applicable approach is to mix microcrystals with reagents at varying time points prior to exposure to the X-ray beam. A powerful approach has been to combine droplet-on-demand ‘tape drive’ sample delivery with X-ray emission spectroscopy (XES) that correlates atomic structure with the electronic states of metal ions within the sample. To the best of our knowledge, such a combined methodology has not been deployed previously on a synchrotron beamline but has been restricted to X-ray free-electron lasers. Here we describe two independent prototype experiments along the development pathway to a combined droplet-on-demand diffraction and XES system on the microfocus synchrotron beamline VMXi at Diamond Light Source. We demonstrate the collection of a high-quality serial diffraction data set from microcrystals within droplets having a volume of hundreds of picolitres deposited on a moving tape. In separate experiments on VMXi, we collected XES data from microcrystals of a copper enzyme delivered using a high-viscosity extruder. Together, these results demonstrate the feasibility of combined droplet-on-demand serial crystallography and XES experiments using a third-generation synchrotron beamline.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;Time-resolved X-ray crystallography is experiencing a resurgence, in part because of serial methods that readily allow scientists to create stop-motion movies of the macromolecular functions of photoactivation, enzyme-catalysed reactions and ligand-induced conformational changes triggering further downstream signalling events. While some reactions can be initiated with light, either naturally or using photocaged compounds, a more generally applicable approach is to mix microcrystals with reagents at varying time points prior to exposure to the X-ray beam. A powerful approach has been to combine droplet-on-demand ‘tape drive’ sample delivery with X-ray emission spectroscopy (XES) that correlates atomic structure with the electronic states of metal ions within the sample. To the best of our knowledge, such a combined methodology has not been deployed previously on a synchrotron beamline but has been restricted to X-ray free-electron lasers. Here we describe two independent prototype experiments along the development pathway to a combined droplet-on-demand diffraction and XES system on the microfocus synchrotron beamline VMXi at Diamond Light Source. We demonstrate the collection of a high-quality serial diffraction data set from microcrystals within droplets having a volume of hundreds of picolitres ","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 635-649"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal clear. Engineering complexity","authors":"Gautam Radhakrishna Desiraju","doi":"10.1107/S2052252526006676","DOIUrl":"10.1107/S2052252526006676","url":null,"abstract":"<div><div>The field of structural chemistry has been significantly reshaped by the development of crystal engineering, a subject focused on the strategic design of molecular solids with specific properties. Central to this advancement is the concept of the supramolecular synthon, the core structural module, which can be identified as a synthetic target. Such thinking enables a retrosynthetic approach to crystal design, allowing for the predictable assembly of organic solids using intermolecular interactions as tactical elements that accompany the design strategy. A major shift in our understanding of molecular architecture occurred through the validation of weak hydrogen bonds – specifically C—H⋯O interactions – as structurally and functionally relevant. Once overlooked, these interactions are now recognized for their essential roles in both small-molecule crystals and complex biological systems. The crystal engineer’s palette of interactions has been further expanded to include halogen bonding and other molecular associations involving electrophilic chalcogen, pnictogen and tetrel atoms, leading to standardized international definitions for these bonds. The culmination of these studies treats the molecular crystal not merely as an assembly of parts, but as a complex, holistic system. By framing the crystal as a supramolecular entity, the field has moved toward a predictive science that balances various intermolecular forces to engineer functional materials.</div></div><div>The field of structural chemistry has been significantly reshaped by the development of crystal engineering, a subject focused on the strategic design of molecular solids with specific properties. Central to this advancement is the concept of the supramolecular synthon, the core structural module, which can be identified as a synthetic target. Such thinking enables a retrosynthetic approach to crystal design, allowing for the predictable assembly of organic solids using intermolecular interactions as tactical elements that accompany the design strategy. A major shift in our understanding of molecular architecture occurred through the validation of weak hydrogen bonds – specifically C—H⋯O interactions – as structurally and functionally relevant. Once overlooked, these interactions are now recognized for their essential roles in both small-molecule crystals and complex biological systems. The crystal engineer’s palette of interactions has been further expanded to include halogen bonding and other molecular associations involving electrophilic chalcogen, pnictogen and tetrel atoms, leading to standardized international definitions for these bonds. The culmination of these studies treats the molecular crystal not merely as an assembly of parts, but as a complex, holistic system. By framing the crystal as a supramolecular entity, the field has moved toward a predictive science that balances various intermolecular forces to engineer functional materials.</div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 527-540"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148411841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying optical scattering losses in pump–probe serial femtosecond crystallography experiments","authors":"Thomas R. M. Barends,&nbsp;Alexander Gorel,&nbsp;Stanisław Niziński,&nbsp;Martin V. Appleby,&nbsp;Marco Kloos,&nbsp;Soshichiro Nagano,&nbsp;Mario Hilpert,&nbsp;Florian Dworkowski,&nbsp;Claudio Cirelli,&nbsp;Emma V. Beale,&nbsp;Elisabeth Hartmann,&nbsp;Camila Bacellar,&nbsp;Robert L. Shoeman,&nbsp;R. Bruce Doak,&nbsp;John H. Beale,&nbsp;Philip J. M. Johnson,&nbsp;Ilme Schlichting","doi":"10.1107/S2052252526005403","DOIUrl":"10.1107/S2052252526005403","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Ultrafast pump–probe serial femtosecond crystallography (SFX) experiments are typically performed with extremely high excitation laser fluence to maximize the occupancy of the light-induced state. This has been justified by assuming that a dominant fraction (up to 99%) of the pump laser light is scattered by the jetting medium, strongly reducing the pump laser fluence in the crystals which, therefore, do not absorb multiple photons and thus undergo the biologically relevant single-photon photoreaction. However, this notion is strongly contested in the field. To address the issue of pump laser scattering losses in high viscosity jets, we performed time-resolved SFX experiments on fatty acid photo­decarboxyl­ase crystals using high-viscosity extrusion (HVE) and both patterned and non-patterned sheet-on-sheet (SOS) fixed-target sample delivery systems on the Cristallina-MX instrument at SwissFEL. Tightly focused pump laser beams were used to mitigate light contamination (the undesired accidental illumination of neighboring crystals) in SOS chips, paving the way for their use in pump–probe investigations of lipidic-cubic-phase-grown membrane protein crystals. Determination of the light-induced reaction intermediate occupancies enabled a comparison of the influence of the delivery method on the pump laser fluence reaching the crystals. We show that optically transparent high-viscosity jets and chip crystal delivery methods result in photoproduct yields that approach 70–80% and 60–70%, respectively, of computationally derived yields that take into account excitation probabilities. These results demonstrate that clear viscous jets scatter pump laser light far less than has been claimed. Consequently, the use of excessive photoexcitation energy densities is neither needed nor justified in optically pumped time-resolved SFX experiments when using appropriately sized crystals.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;Ultrafast pump–probe serial femtosecond crystallography (SFX) experiments are typically performed with extremely high excitation laser fluence to maximize the occupancy of the light-induced state. This has been justified by assuming that a dominant fraction (up to 99%) of the pump laser light is scattered by the jetting medium, strongly reducing the pump laser fluence in the crystals which, therefore, do not absorb multiple photons and thus undergo the biologically relevant single-photon photoreaction. However, this notion is strongly contested in the field. To address the issue of pump laser scattering losses in high viscosity jets, we performed time-resolved SFX experiments on fatty acid photo­decarboxyl­ase crystals using high-viscosity extrusion (HVE) and both patterned and non-patterned sheet-on-sheet (SOS) fixed-target sample delivery systems on the Cristallina-MX instrument at SwissFEL. Tightly focused pump laser beams were used to mitigate light contamination (the undesired accidental illumination of neighboring crystals) in SOS chips, paving the way","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 606-622"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148455838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpreting wide-angle X-ray scattering data using DNA duplexes as model systems","authors":"Qingyue Hu,&nbsp;Vera Amirbekian,&nbsp;Sarah Uttormark,&nbsp;Hugh Robert Higinbotham,&nbsp;Lois Pollack","doi":"10.1107/S2052252526007700","DOIUrl":"10.1107/S2052252526007700","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Small-angle X-ray scattering (SAXS) provides important information about global biomolecular solution structures yet is resolution limited. Extension to higher scattering angles through wide-angle X-ray scattering (WAXS) extends the resolution of solution measurements to single ångströms; however, interpretation of WAXS profiles is challenging. Here we establish a practical framework for interpreting WAXS measurements in terms of repeated real-space distances and specific structural motifs in nucleic acids. We compare experimentally measured scattering profiles from two 25-base-pair DNA duplexes, an AT-rich construct and a mixed-sequence duplex. Their SAXS profiles are similar but they exhibit strikingly different WAXS signatures. By systematically varying the reciprocal-space cutoff prior to indirect Fourier transforms, we show how increasing information content sharpens real-space resolution and reveals periodic features associated with base stacking and duplex geometry. Real-space distance distributions identify the dominant atomic contributors to these features and directly connect them to backbone separations, groove widths, and long-range stacking periodicities that vary in a sequence-dependent manner. Together, these results establish WAXS as a powerful tool for probing nucleic acid architecture and, in conjunction with time-resolved measurements, dynamics, and demonstrate that WAXS measurements provide a robust and generalizable route to extracting high-resolution structural information from solution measurements.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;Small-angle X-ray scattering (SAXS) provides important information about global biomolecular solution structures yet is resolution limited. Extension to higher scattering angles through wide-angle X-ray scattering (WAXS) extends the resolution of solution measurements to single ångströms; however, interpretation of WAXS profiles is challenging. Here we establish a practical framework for interpreting WAXS measurements in terms of repeated real-space distances and specific structural motifs in nucleic acids. We compare experimentally measured scattering profiles from two 25-base-pair DNA duplexes, an AT-rich construct and a mixed-sequence duplex. Their SAXS profiles are similar but they exhibit strikingly different WAXS signatures. By systematically varying the reciprocal-space cutoff prior to indirect Fourier transforms, we show how increasing information content sharpens real-space resolution and reveals periodic features associated with base stacking and duplex geometry. Real-space distance distributions identify the dominant atomic contributors to these features and directly connect them to backbone separations, groove widths, and long-range stacking periodicities that vary in a sequence-dependent manner. Together, these results establish WAXS as a powerful tool for probing nucleic acid architecture and, in conjunction with time-resolved measurements, dynamics, and demonstrate that WAXS measurements ","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 650-658"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148864981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CryoEM in the fast lane of structural biology.","authors":"Richard Henderson, S Samar Hasnain","doi":"10.1107/S2052252526007220","DOIUrl":"10.1107/S2052252526007220","url":null,"abstract":"<p><p>Single-particle cryoEM has made visualization of biological molecules and their complexes at high resolution possible without the need for crystallization. The last decade has seen a rapid growth in the number of structures determined by cryoEM; for membrane proteins, the total number of cryoEM structures has exceeded that determined by crystallography.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"523-526"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13548829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562165","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":"Simple and robust aqueous sheet jets in vacuum","authors":"Patrick E. Konold,&nbsp;Adil Ansari,&nbsp;Daniel Westphal,&nbsp;Patrick Adams,&nbsp;Romain Letrun,&nbsp;Joana Valerio,&nbsp;Johan Bielecki,&nbsp;Roberto C. Alvarez,&nbsp;Szabolcs Bódizs,&nbsp;Katerina Dörner,&nbsp;Gabriel Ducrocq,&nbsp;Lukas Grunewald,&nbsp;Konstantin Kharitonov,&nbsp;Chan Kim,&nbsp;Marco Kloos,&nbsp;Anna Králová,&nbsp;Taru Larkiala,&nbsp;Michael Maihöfer,&nbsp;Dimitra Manatou,&nbsp;Robert Mehlig,&nbsp;Filipe R. N. C. Maia","doi":"10.1107/S2052252526007013","DOIUrl":"10.1107/S2052252526007013","url":null,"abstract":"<div><div>Free-standing thin liquid films offer a convenient way to probe matter in solution without a substrate, where a small sample thickness is required. The production of thin films in a vacuum environment is required for probes that cannot penetrate through a surrounding gas or in cases where the gas produces problematic background noise. Nozzles that produce continuously flowing liquid sheet jets have been employed recently for scattering and spectroscopy measurements at X-ray free-electron lasers (XFELs). However, their performance in vacuum with aqueous samples is complicated by high freezing susceptibility due to a strong evaporative cooling effect. Here, we introduce a vacuum-compatible gas-impinging liquid sheet jet nozzle capable of generating sub-100 nm aqueous films. The introduction of a second axisymmetric helium gas sheath surrounding the liquid orifice enables seamless startup and shutdown within a vacuum environment. We investigated the sheet geometry dependence under varying flow conditions and liquid viscosity and demonstrated its viability for X-ray scattering measurements at a high-repetition-rate XFEL source. Finally, we present potential strategies for reducing sample consumption. Our findings confirm that this nozzle exhibits simplified vacuum operation and may help promote the broader utilization of liquid sheet jets for several experimental applications.</div></div><div>Free-standing thin liquid films offer a convenient way to probe matter in solution without a substrate, where a small sample thickness is required. The production of thin films in a vacuum environment is required for probes that cannot penetrate through a surrounding gas or in cases where the gas produces problematic background noise. Nozzles that produce continuously flowing liquid sheet jets have been employed recently for scattering and spectroscopy measurements at X-ray free-electron lasers (XFELs). However, their performance in vacuum with aqueous samples is complicated by high freezing susceptibility due to a strong evaporative cooling effect. Here, we introduce a vacuum-compatible gas-impinging liquid sheet jet nozzle capable of generating sub-100 nm aqueous films. The introduction of a second axisymmetric helium gas sheath surrounding the liquid orifice enables seamless startup and shutdown within a vacuum environment. We investigated the sheet geometry dependence under varying flow conditions and liquid viscosity and demonstrated its viability for X-ray scattering measurements at a high-repetition-rate XFEL source. Finally, we present potential strategies for reducing sample consumption. Our findings confirm that this nozzle exhibits simplified vacuum operation and may help promote the broader utilization of liquid sheet jets for several experimental applications.</div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 659-667"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148864979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A discussion of cryo-EM terminology as the outreach and number of PDB entries expand","authors":"Bruno P. Klaholz","doi":"10.1107/S2052252526007505","DOIUrl":"10.1107/S2052252526007505","url":null,"abstract":"<div><div>Cryo electron microscopy (cryo-EM) has made great advances in the last decade, progressively increasing its impact in structural biology as a key method to address molecular structures and mechanisms of various macromolecular complexes. Single-particle cryo-EM will soon equal the number of yearly entries in the Protein Data Bank from structures determined by X-ray crystallography. This is largely thanks to improved cryo electron microscope instrumentation and advanced image-processing tools and structure-sorting methods. As the role of cryo-EM is expanding to an increasingly large community, including newcomers and scientists joining from related fields, it is timely to revisit some fundamental concepts and basics of single-particle cryo-EM and image processing as terminology has become less well defined and, in some cases, confusing. Here we summarize and define some typical terms important for understanding the underlying physical concepts. These include ‘cryo-EM’, ‘cryo-ET’, ‘3D reconstruction’, ‘coarsening’, ‘contour level’ and others. We also discuss resolution estimation and map deposition.</div></div><div>Cryo electron microscopy (cryo-EM) has made great advances in the last decade, progressively increasing its impact in structural biology as a key method to address molecular structures and mechanisms of various macromolecular complexes. Single-particle cryo-EM will soon equal the number of yearly entries in the Protein Data Bank from structures determined by X-ray crystallography. This is largely thanks to improved cryo electron microscope instrumentation and advanced image-processing tools and structure-sorting methods. As the role of cryo-EM is expanding to an increasingly large community, including newcomers and scientists joining from related fields, it is timely to revisit some fundamental concepts and basics of single-particle cryo-EM and image processing as terminology has become less well defined and, in some cases, confusing. Here we summarize and define some typical terms important for understanding the underlying physical concepts. These include ‘cryo-EM’, ‘cryo-ET’, ‘3D reconstruction’, ‘coarsening’, ‘contour level’ and others. We also discuss resolution estimation and map deposition.</div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 580-588"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}