IUCrJ最新文献

{"title":"Linear-scaling aspherical crystallographic refinement of proteins: a case study for crambin and rubredoxin","authors":"Justin Bergmann ,&nbsp;Florian Kleemiss ,&nbsp;Joel Creutzberg ,&nbsp;Esko Oksanen ,&nbsp;Ulf Ryde","doi":"10.1107/S2052252525010188","DOIUrl":"10.1107/S2052252525010188","url":null,"abstract":"<div><div>Linear-scaling fragment Hirshfeld atom refinement has been implemented in <em>Olex2</em> within the <em>NoSpherA2</em> interface, which also solved previous issues with hydrogen bonds. This allowed the refinement of two small proteins, crambin and rubredoxin (the latter including a metal site), with quantum mechanical aspherical atomic form factors.</div></div><div><div>Hirshfeld atom refinement (HAR) provides a more realistic interpretation of crystallographic data than the standard independent atom model (IAM) by using aspherical atomic form factors derived from quantum mechanical (QM) calculations. With this aspherical description, it is possible to obtain improved atomic positions, atomic displacement parameters and correct bond lengths even for hydrogen atoms. Unfortunately, HAR is computationally very demanding for larger molecules. Recently, we suggested how this can be solved by calculating aspherical atomic form factors for small overlapping fragments of the system, the fragHAR approach. Here, we have created a new implementation of fragHAR in <em>Olex2</em> within the <em>NoSpherA2</em> interface. We have also solved previous issues with hydrogen bonds by automatically extending the fragments with all hydrogen-bond acceptors. This implementation was successfully tested on three oligopeptides, demonstrating that fragHAR yields indistinguishable results in terms of atomic charge, residual density or <em>R</em> values compared with full HAR. Subsequently, fragHAR was applied to the proteins crambin and rubredoxin, with 843 and 1014 atoms, respectively, showing improved results in terms of <em>e</em>_gross, which decreases from 0.350 with the IAM to 0.318 with fragHAR for crambin, and from 0.195 to 0.176 for rubredoxin, although it turned out to be necessary to keep all bond lengths involving hydrogen atoms constrained for the latter protein. FragHAR shows near-linear scaling and 46-fold speedup for rubredoxin compared with HAR. It also provides a convenient solution to alternative conformations and positional disorder, which cause an exponential increase in the time consumption of the conventional HAR approach. The successful refinement of rubredoxin marks a significant milestone, presenting the first HAR application of a metalloprotein, and further underlines the relevance of fragHAR in protein crystallography.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 53-62"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145742728","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":"IUCrJ in 2025 - welcomes, farewells and special issues.","authors":"Andrew J Allen","doi":"10.1107/S2052252525011194","DOIUrl":"https://doi.org/10.1107/S2052252525011194","url":null,"abstract":"<p><p>As we start a new year, it is timely to welcome two new Main Editors of IUCrJ and bid farewell to those who have stepped down, as well as highlight a couple of ongoing developments of interest to IUCrJ readers and authors.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889097","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":"Broadband high-resolution X-ray ptychography system spanning tender to hard X-ray regimes","authors":"Yuhei Sasaki ,&nbsp;Nozomu Ishiguro ,&nbsp;Masaki Abe ,&nbsp;Shuntaro Takazawa ,&nbsp;Hideshi Uematsu ,&nbsp;Naru Okawa ,&nbsp;Fusae Kaneko ,&nbsp;Yukio Takahashi","doi":"10.1107/S2052252525009236","DOIUrl":"10.1107/S2052252525009236","url":null,"abstract":"<div><div>An advanced X-ray ptychography system has been developed that facilitates nanoscale imaging across both tender and hard X-ray regions using a single optical setup.</div></div><div><div>X-ray ptychography is a high-resolution imaging technique capable of resolving nanoscale structures and probing chemical states. However, despite advances, most conventional X-ray ptychography systems have been designed to operate within a single energy regime, such as hard (&gt; 5 keV), soft (&lt; 2 keV) or tender (2–5 keV) X-rays. We have developed a high-efficiency achromatic ptychographic measurement system on beamline BL10U at NanoTerasu, a 3 GeV synchrotron radiation facility in Japan, that incorporates advanced Kirkpatrick–Baez focusing mirrors and a high-speed CITIUS detector. Utilizing this innovative system, we have successfully reconstructed phase images with a spatial resolution exceeding 50 nm from 200 nm-thick tantalum test charts at X-ray energies of 2.5, 5.0 and 7.5 keV. We have performed energy scans around the Ca and S <em>K</em> edges on CaSO₄·2H₂O particles to demonstrate the spectromicroscopic capabilities of the system. The reconstructed images provide spatially resolved X-ray absorption spectra, revealing distinct edge features. This system not only enables element-specific imaging across the tender to hard X-ray spectrum but is also particularly advantageous for light-element materials, which benefit from enhanced phase contrast in the tender X-ray range. This advancement opens up new possibilities for <em>in situ</em> imaging of complex chemical environments in energy devices and biological specimens.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 11-18"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145451901","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":"Obtaining single crystals containing cationic porphyrins from aqueous solutions: a systematic approach including nano-crystallization, organic modifiers and gel crystallization","authors":"Rayk A. Schmitz ,&nbsp;Florian C. Brunner ,&nbsp;Leonard P. Zelder ,&nbsp;Bernhard Spingler","doi":"10.1107/S2052252525009716","DOIUrl":"10.1107/S2052252525009716","url":null,"abstract":"<div><div>A stepwise guide to the crystallization of charged molecules from aqueous solutions is presented.</div></div><div><div>Obtaining high-quality single crystals containing charged molecules from aqueous solutions can sometimes be challenging. In this publication, we studied the crystallization of polycationic porphyrins. Crystals of three polycationic porphyrins, [5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)porphyrin, 5-(4-cyanophenyl)-10,15,20-tris(1-methylpyridin-1-ium-4-yl)porphyrin and 5-(4-carboxy­phenyl)-10,15,20-tris(1-methylpyridin-1-ium-4-yl)porphyrin], were obtained with different anions. We started initially with ‘nano-crystallization’ screening in order to identify promising combinations of the cations with suitable anions, followed by optimizing the ratio of anions to cations. Both steps yielded crystals, leading to the determination of one porphyrin-containing crystal structure from each step. In the next step, five different organic solvents were trialled as additives in an aqueous hanging-drop crystallization setup, which led to the determination of three more crystal structures. It was shown that it was possible to improve the quality of the crystals without the organic additive being incorporated into the crystal structure. Finally, crystals of one porphyrin salt were obtained by gel crystallization. These crystals were higher quality than the crystal grown by vapour diffusion, leading to a high-quality and higher-resolution X-ray structure determination. This is the first porphyrin structure to be determined from a crystal grown by gel crystallizaton.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 44-52"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653693","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":"Phase transitions in rutile-related V0.92O2 synthesized at high pressures and tem­per­a­tures","authors":"Andrzej Grzechnik ,&nbsp;Václav Petříček ,&nbsp;Pascal Reiss ,&nbsp;Paul Zakalek ,&nbsp;Dmitry Chernyshov ,&nbsp;Karen Friese","doi":"10.1107/S2052252525010693","DOIUrl":"10.1107/S2052252525010693","url":null,"abstract":"<div><div>Phase transitions in metastable rutile-related V_0.92O₂ were studied with single-crystal X-ray diffraction and measurements of electronic transport properties at extreme conditions. The high-tem­per­a­ture incommensurate phase was found to be insulating.</div></div><div><div>Structural phase transitions in metastable rutile-related V_0.92O₂ synthesized at 10 GPa and 1273 K were studied with single-crystal X-ray diffraction in the tem­per­a­ture range 110–500 K and at pressures up to 9.2 GPa. V_0.92O₂ starts to decom­pose at 470 K and atmospheric pressure. When heated to tem­per­a­tures above about 350 K, the material transforms to an incommensurate phase. The oxygen sublattice is essentially rigid and it is mostly the V atoms that are affected by the modulation. An anharmonic description of the displacement parameters and their corresponding modulation is used for the V atoms to reach satisfactory agreement factors for main and first-order satellite reflections, indicating substantial disorder in the modulated structure. Measurements of electronic transport properties provide evidence that the incommensurate phase is insulating. On com­pression at room tem­per­a­ture, V_0.92O₂ reaches the ideal rutile structure at about 5.0 GPa. Both structural and electronic phase transitions are of the first-order character. The results of this work demonstrate that the structural and electronic behaviour of V_0.92O₂ at extreme conditions is distinctly different from that of stoichiometric VO₂.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 116-125"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145819171","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":"Radiation damage and the case for unpatterned fixed targets","authors":"Dominik Oberthür","doi":"10.1107/S2052252525011418","DOIUrl":"10.1107/S2052252525011418","url":null,"abstract":"<div><div>Advances in serial crystallography have reshaped approaches to radiation damage at room temperature. This commentary highlights recent work comparing XFEL and synchrotron experiments, emphasizing its implications for serial crystallography at modern X-ray sources.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 3-5"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889092","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":"Structure of the bacteriophage PhiKZ non-virion RNA polymerase bound to a p119L open promoter analogue","authors":"Chao-Sheng Chen ,&nbsp;Natàlia de Martín Garrido ,&nbsp;Maria Yakunina ,&nbsp;Christopher H. S. Aylett","doi":"10.1107/S2052252525009273","DOIUrl":"10.1107/S2052252525009273","url":null,"abstract":"<div><div>Bacteriophage ΦKZ is a massive bacterial virus with potential as a therapy for <em>Pseudomonas aeruginosa</em>, which forms a bacteriophage nucleus in infected cells to exclude the host immune system, and transcribes its genes with its own, non-canonical multi-subunit RNA polymerase. The structure of this polymerase in the process of binding an analogue of its cognate promoter is resolved, revealing an unanticipated method of promoter consensus recognition involving the β-like, rather than the σ-factor-like subunit.</div></div><div><div>Bacteriophage ΦKZ (PhiKZ) was the first identified member of a family of massive bacterial viruses. ΦKZ infects <em>Pseudomonas aeruginosa</em>, which kills tens of thousands every year, and it therefore has potential as a bacteriophage therapy. On infection, ΦKZ forms a ‘nucleus’ to protect its genome by excluding host immune systems. This barrier means that it has had to become independent of the host transcriptional apparatus; it cannot simply recruit the host RNA polymerase (RNAP) to its promoters as it is excluded from the viral DNA, and therefore it expresses and imports its own non-virion RNA polymerase (nvRNAP). The ΦKZ nvRNAP, and related jumbo-phage RNAPs including that from bacteriophage AR9, are particularly noteworthy. Unlike typical viral RNAPs which are formed as only a single subunit, it is a non-canonical multi-subunit RNAP directly related to those from eubacteria, and more distantly eukaryotes and archaea. It encompasses four proteins representing patchwork homologues of the eubacterial β/β′ subunits, and a fifth that appears to have evolved from a σ factor, but no homologues of the α or ω subunits required for formation of a catalytically active complex in eubacterial RNAPs. Its mechanism of promoter recognition is also highly divergent; transcription is initiated from a site marked only by a tiny four-base consensus sequence co-located with the start site. We have resolved the structure of the ΦKZ nvRNAP bound to an open analogue of its cognate promoter, p119L, revealing that while the σ-factor-like subunit GP68 is involved in bubble stabilization, the sequence-specific promoter consensus sequence is bound between the lobe of the β-subunit homologue GP123 and the enzymatic core of the complex. Our results shed light on the differences between mechanisms of promoter recognition in the ΦKZ nvRNAP and canonical eubacterial RNAPs, and on the uniquely specialized features of bacteriophage transcriptional apparatuses in general.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 31-43"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145482101","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":"Anisotropic diffraction of materials with fibre symmetry: application to chitin cuticle","authors":"Yanhong Wang ,&nbsp;Tim Snow ,&nbsp;Nick Terrill ,&nbsp;Himadri Shikhar Gupta","doi":"10.1107/S2052252525009686","DOIUrl":"10.1107/S2052252525009686","url":null,"abstract":"<div><div>A generalized diffraction model is presented for anisotropic nanomaterials with fibre symmetry, enabling the extraction of 3D orientation, strain and angular dispersion from wide-angle X-ray scattering patterns without sample rotation. Validated on chitinous Bouligand structures in shrimp cuticle, this framework allows robust multi-reflection analysis and is broadly applicable to complex biological and synthetic fibre-based materials.</div></div><div><div>Understanding the structure–function relationships in anisotropic fibre-symmetric materials is critical for both biological insight and bioinspired design. We present a generalized analytical model for X-ray diffraction intensity from nanofibrillar materials with fibre symmetry, accommodating arbitrary diffraction rings beyond prior axial and equatorial limits. This model integrates 3D orientation, strain heterogeneity and angular misalignment effects, and is validated using wide-angle X-ray diffraction (WAXD) from the Bouligand-structured cuticle of the mantis shrimp (<em>Odontodactylus scyllarus</em>). Using scanning synchrotron WAXD, we extract depth-averaged and sub-lamellar information on 3D fibre orientation and crystalline parameters from 2D scans. Model simulations and experimental fits show accurate reconstruction of the Bouligand texture and reveal spatial gradients in orientation, strain and angular dispersion. By fitting multiple reflections – axial (002), equatorial (110) and intermediate (013) – we improve the robustness in parameter extraction, especially in regions where the Ewald condition is partially satisfied. Our framework enhances the interpretation of WAXD in heterogeneous fibre-based materials and can be embedded into advanced tomographic or machine-learning workflows. This approach is applicable to a broad class of biological and synthetic composites, facilitating high-throughput structural characterization in scenarios where rotation is impractical or impossible.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 63-76"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145794001","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":"AutoLEI: An XDS-based pipeline with graphical user interface for automated real-time and offline batch 3D ED/microED data processing","authors":"Lei Wang ,&nbsp;Yinlin Chen ,&nbsp;Emma Scaletti Hutchinson ,&nbsp;Pål Stenmark ,&nbsp;Gerhard Hofer ,&nbsp;Hongyi Xu ,&nbsp;Xiaodong Zou","doi":"10.1107/S2052252525010784","DOIUrl":"10.1107/S2052252525010784","url":null,"abstract":"<div><div>A pipeline with a graphical user interface for real-time and offline 3D ED/microED data processing by <em>XDS</em> was developed. The pipeline aims to improve efficiency, minimize redundant data processing work and provide users with real-time feedback during data collection.</div></div><div><div>Three-dimensional electron diffraction (3D ED), also known as microcrystal electron diffraction (microED), is an emerging method for determining structures from submicron-sized crystals. With the development of rapid and convenient data collection protocols, acquiring dozens of datasets in a single 3D ED/microED session has become routine. A fast and automated workflow for processing, scaling and merging a large number of 3D ED/microED datasets can significantly accelerate the structure determination process. Herein, we present an <em>XDS</em>-based pipeline with a graphical user interface for automated real-time and offline batch 3D ED/microED data processing (<em>AutoLEI</em>). We demonstrate the functionality and applications of the pipeline through four examples, using both offline and real-time data processing capabilities. The samples include small organic molecules, metal–organic frameworks (MOFs) and proteins, showcasing the versatility and efficiency of <em>AutoLEI</em> in various applications.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 105-115"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145810188","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":"Exploring fibers with X-ray eyes","authors":"Cinzia Giannini","doi":"10.1107/S2052252525011182","DOIUrl":"10.1107/S2052252525011182","url":null,"abstract":"<div><div>The novel analytical approach for interpreting complex X-ray diffraction patterns from fibers described by Wang <em>et al.</em> [<span>(2026), IUCrJ, 13, 63–76</span>] is discussed.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 8-10"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889082","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}