IUCrJ最新文献

{"title":"Making sense of invisible densities in single-particle cryo-EM.","authors":"Xiaoxuan Lin, Yifan Cheng","doi":"10.1107/S2052252526002952","DOIUrl":"10.1107/S2052252526002952","url":null,"abstract":"<p><p>In the era of single-particle cryogenic electron microscopy (cryo-EM) and AI-driven protein structure prediction, obtaining high-resolution protein structures, either experimentally or computationally, has become increasingly routine. Yet studying and understanding protein dynamics remains challenging. In single-particle cryo-EM, protein dynamics are most obviously manifested as poor local resolution or disappearing densities in specific regions of a reconstruction. No method is yet available to computationally generate conformational ensembles that fully deconvolute these experimental observations. When dynamics are key to understanding protein function, it is clear to us that introducing new experimental approaches is necessary to close this gap and make sense of invisible densities in single-particle cryo-EM.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"217-220"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147771953","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":"Modelling of radiation damage and beam-induced heating of room-temperature samples at extremely high flux MX beamlines","authors":"Martin V. Appleby ,&nbsp;Michal W. Kepa ,&nbsp;Graeme Winter ,&nbsp;Katherine E. McAuley ,&nbsp;John H. Beale","doi":"10.1107/S2052252525011224","DOIUrl":"10.1107/S2052252525011224","url":null,"abstract":"<div><div>Modelling of radiation damage and beam-induced heating at extremely high flux macromolecular crystallography beamlines is presented.</div></div><div><div>The upgrade of the third-generation synchrotrons to diffraction-limited storage rings will enable a gain of up to two orders of magnitude in brilliance and further enable the creation of multiple macromolecular crystallography (MX) beamlines capable of delivering fluxes in excess of 1 × 10¹⁵ photons s⁻¹, here called extremely high flux (EHF) MX beamlines. These beamlines, such as ID29 at ESRF-EBS, BioCARS at APS-U and MicroMAX at MAX IV, have all been either partly or solely geared towards delivering time-resolved MX experiments at room temperature and realizing microsecond time resolutions. Given the uncharted territory of using dose rates in excess of 50 GGy s⁻¹ at many facilities, this article examines some of the expected consequences, suggesting that considerable attention should be paid to beam heating effects for crystals &lt;20 µm exposed to 1 × 10¹⁵ photons s⁻¹. Several strategies have been proposed to mitigate heating effects when high dose rates are required for a time-resolved experiment, including reducing the absorbed dose by increasing the size of the crystal and the beam profile, and explicitly exploiting the motion of the crystal in serial crystallography delivery systems. The model presented here is intended to serve as a useful tool to inform experimental design and support users’ decision making in such cases.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 184-197"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165401","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":"Application of differential scanning fluorimetry to X-ray protein crystallography","authors":"Yukari Sato ,&nbsp;Toshiya Senda","doi":"10.1107/S2052252526000072","DOIUrl":"10.1107/S2052252526000072","url":null,"abstract":"<div><div>Differential scanning fluorimetry (DSF) assesses protein thermal stability in solution using a standard real-time PCR instrument. Optimizing the protein buffer composition and crystallization conditions through DSF can significantly enhance crystal quality.</div></div><div><div>X-ray crystallography remains a powerful technique for determining high-resolution protein structures; however, obtaining high-quality crystals is a significant bottleneck. This study presents a detailed experimental workflow that employs differential scanning fluorimetry (DSF) to optimize protein crystallization. DSF, which measures protein thermal stability, was used to refine both protein buffer composition and crystallization conditions. The method was applied to two distinct proteins: CreD, a nitrosuccinate lyase, and HIRA, a histone chaperone. For CreD, DSF-based optimization of the protein buffer enhanced the crystal quality, increasing the resolution from 3.32 to 2.18 Å. For HIRA(644–1017), DSF-guided optimization of the protein buffer significantly improved the protein solubility from 0.1 to 19.1 mg ml⁻¹, facilitating the growth of initial crystals. Further optimization of the crystallization conditions using DSF, combined with microseeding, improved the crystal quality, leading to structure determination at 2.45 Å resolution. This study demonstrates that DSF is a valuable tool for efficiently optimizing protein crystallization. The workflow presented here, involving initial DSF-based optimization of protein buffers followed by DSF-guided optimization of crystallization conditions, offers a rational approach to enhancing protein crystal quality, thereby facilitating structure determination by X-ray crystallography.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 169-183"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146105507","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":"Round robin on structure analysis from 3D electron diffraction data","authors":"Mauro Gemmi ,&nbsp;Lukáš Palatinus ,&nbsp;Philippe Boullay ,&nbsp;Jan Pieter Abrahams ,&nbsp;Amatassalâm Ben Meriem ,&nbsp;Erica Cordero-Oyonarte ,&nbsp;Vincentia Emerson Agbemeh ,&nbsp;Hrushikesh Chintakindi ,&nbsp;Moussa Diame Faye Diouf ,&nbsp;Pavel Filipcik ,&nbsp;Laura Gemmrich Hernandéz ,&nbsp;Eric van Genderen ,&nbsp;Joke Hadermann ,&nbsp;Amirhossein Hajizadeh ,&nbsp;Branislav Jeriga ,&nbsp;Ute Kolb ,&nbsp;Senik Matinyan ,&nbsp;Sara Passuti ,&nbsp;Marco Santucci ,&nbsp;Ashwin Suresh ,&nbsp;Xiaodong Zou","doi":"10.1107/S205225252600045X","DOIUrl":"10.1107/S205225252600045X","url":null,"abstract":"<div><div>This blind test uses three known samples to determine the accuracy limits of 3D electron diffraction and to assess various challenges. The study aims to evaluate how well different users with diverse experimental setups can perform tasks such as hydrogen-atom detection, mixed occupancy analysis and absolute structure determination. By comparing results across multiple participants and platforms, we can gauge the reliability of the method and identify potential areas for improvement in 3D electron diffraction techniques.</div></div><div><div>3D electron diffraction (3D ED) has undergone impressive development in the last decade. However, its accuracy and reproducibility have never been tested, up to now, in different laboratories on the same batch of samples. This paper reports a round robin on three test structures, two inorganic and one organic, solved and refined with 3D ED in seven different laboratories employing different transmission electron microscopes, with different acceleration voltages, different methodologies and different detectors. The results of the round robin show a remarkable accuracy of the technique that, in the case of kinematical refinement, is around 0.05 Å error on atomic positions for the inorganic samples and 0.15 Å for the beam-sensitive organic crystal. Dynamical refinement further improves the accuracy. The analysis of diverse samples and numerous data sets again confirms that dynamical refinement is a well established procedure, significantly reducing the refinement <em>R</em> factors, improving the accuracy of the structure models in most cases, and providing fine structural details, such as hydrogen-atom positions and the absolute structure, for both inorganic and organic samples.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 198-210"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146179721","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":"3D ED: Accessible, robust and accurate","authors":"Stéphanie Kodjikian","doi":"10.1107/S2052252526001855","DOIUrl":"10.1107/S2052252526001855","url":null,"abstract":"<div><div>Now a common technique in crystallography, three-dimensional electron diffraction (3D ED) is on track to bridge the gap with X-ray diffraction in terms of structural accuracy.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 130-131"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326122","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":"Stereochemical aspects of the nucleophilic attack in different classes of l-asparaginases","authors":"Miroslaw Gilski ,&nbsp;Kinga Pokrywka ,&nbsp;Mariusz Jaskolski","doi":"10.1107/S2052252525010826","DOIUrl":"10.1107/S2052252525010826","url":null,"abstract":"<div><div>Stereochemical analysis based on the principle of structure correlations has been carried out to identify the primary nucleophile residue in each of the three classes of <span>l</span>-asparaginases and in a group of classless enzymes, helping to confirm their classification.</div></div><div><div><span>l</span>-Asparaginases hydrolyze <span>l</span>-asparagine to <span>l</span>-aspartate with the release of ammonia. Currently, three completely unrelated structural classes of <span>l</span>-asparaginases are known, further subdivided into five types. In each class, the hydrolysis reaction is thought to proceed via a nucleophilic attack of an activated Thr or Ser residue on the carbonyl C<em>sp</em>² atom of the substrate amide group. With the possible exception of class 2 <span>l</span>-asparaginases, which function as N-terminal nucleophile (Ntn) hydro­lases, the identity of the nucleophilic residue is, or at least has been historically, the subject of some controversy, and even in class 2 this issue may not be so entirely obvious. Structural chemistry has, however, excellent tools to figure out reaction mechanisms, based on the application of Bürgi’s structure correlation method (SCM). Its principle allows one to predict the reaction trajectory if sufficient structural (crystallographic) examples of the reagents along the reaction path are known. With respect to the nucleophilic attack on a carbonyl group, the stereochemistry is governed by the nucleophile⋯electrophile distance and the Bürgi–Dunitz angle, later supplemented with the Flippin–Lodge angle. The latter angle is shown to be a poor parameter and is better replaced by the Herschlag dihedral between the planes of the attacking nucleophile and the attacked electrophile. In structural enzymology, applicability of the SCM principle requires the availability of structural examples of the enzyme in question in complex with the substrate or product of the catalytic reaction. In this work, we applied the SCM concept to the three classes of <span>l</span>-asparaginases, identifying in each case the most probable nucleophilic residue as Thr12 in EcAII (class 1), Thr179 in EcAIII (class 2) and Ser48 in ReAV (class 3). In addition, we applied the SCM analysis to the newly identified group of asparaginases without proper classification, called short-chain asparaginases, providing a basis for their proper affiliation in class 1. Finally, the SCM analysis shows that the chirality of the nucleophilic attack in class 2 asparaginases (pro-<em>R</em>) is opposite to that in all other asparaginases.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 132-145"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145989202","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":"Catching new modulated high-pressure phases of δ-chlorpropamide: when the experimental setup matters","authors":"Nikita E. Bogdanov ,&nbsp;Sergey V. Rashchenko ,&nbsp;Boris A. Zakharov ,&nbsp;Yurii V. Seryotkin ,&nbsp;Elena V. Boldyreva","doi":"10.1107/S2052252525011601","DOIUrl":"10.1107/S2052252525011601","url":null,"abstract":"<div><div>Commensurately and incommensurately modulated phases of chlorpropamide have been obtained for the first time on hydro­static compression of its δ polymorph.</div></div><div><div>The antidiabetic drug chlorpropamide [1-(4-chlorophenyl)sulfonyl-3-propyl­urea, CPA] has one of the highest numbers of reported polymorphs, making it an excellent model system for studying structural responses to pressure or temperature. The densest polymorph, δ-CPA, was probed by single-crystal X-ray diffraction at both laboratory and synchrotron facilities. A new high-pressure phase with tripled cell parameter <em>b</em> as compared with the ambient pressure phase was discovered. High-brilliance synchrotron sources and fast data collection strategies allowed us to also detect the formation of the intermediate incommensurately modulated phase at 2.37 (5) GPa. The experiments revealed the effect of the pressure-increasing protocol on the structure evolution on hydro­static compression. The importance and necessity of conducting both laboratory and synchrotron experiments for the same compound when studying solid-state transformations is illustrated. The opportunities provided by synchrotron sources for studying phase transformations are discussed, together with specific characteristics of synchrotron experiments that should not be overlooked.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 146-158"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146010654","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":"Kinetic effects yield different results on the timescales of laboratory and synchrotron high-pressure experiments","authors":"Julien Haines","doi":"10.1107/S2052252526001569","DOIUrl":"10.1107/S2052252526001569","url":null,"abstract":"<div><div>Kinetic effects can be a critical factor in the study of high-pressure phase transitions. X-ray diffraction experiments on the timescales of the laboratory and the synchrotron can provide complementary results on such transformations.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 128-129"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147325770","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":"Automated microbatch-under-oil phase diagrams to rationalize serial crystallography sample preparation","authors":"Jack Stubbs ,&nbsp;Courtney J. Tremlett ,&nbsp;Abigail Waitman ,&nbsp;Nicholas J. Harmer ,&nbsp;Allen M. Orville ,&nbsp;Ivo Tews ,&nbsp;Stefan Kolek ,&nbsp;Patrick D. Shaw Stewart","doi":"10.1107/S2052252526000448","DOIUrl":"10.1107/S2052252526000448","url":null,"abstract":"&lt;div&gt;&lt;div&gt;An automated, low-volume microbatch-under-oil crystallization approach is described that rapidly maps phase diagram boundaries. This approach rationalizes the production of microcrystal suspensions for serial crystallography by explicitly distinguishing metastable from nucleation zones, thereby replacing empirical trial and error with a quantitative guide to sample optimization.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;An automated, low-volume microbatch-under-oil crystallization approach is described that rapidly maps phase diagram boundaries. This approach rationalizes the production of microcrystal suspensions for serial crystallography by explicitly distinguishing metastable from nucleation zones, thereby replacing empirical trial and error with a quantitative guide to sample optimization.&lt;/div&gt;&lt;div&gt;&lt;div&gt;Serial crystallography relies on the reproducible production of high-density suspensions of microcrystals, yet sample optimization remains a resource-intensive bottleneck. While phase diagrams provide a theoretical framework for controlling crystal size and number, experimental mapping is traditionally hindered by relatively high sample consumption. We present an automated microbatch-under-oil crystallization approach that rapidly maps phase boundaries using only 15–60 µl (∼0.15–3.8 mg) of protein. While this workflow is ideally suited for refining existing hits, it serves as a standalone platform for characterizing the crystallization landscape of new protein targets. The power of this approach lies in the integration of three distinct strategies that exploit the stable chemical environment of microbatch-under-oil. Firstly, we utilize an ingenious diagonal sampling strategy that traverses the phase boundary parallel to the solubility curve by systematically varying protein-to-precipitant ratios, identifying primary nucleation zones with far greater efficiency than traditional orthogonal grids. Secondly, we employ a linked variation of multiple precipitants to reveal morphology-specific regions, such as the rod versus plate transitions crucial for time-resolved experiments. Finally, we incorporate automated seed-stock titration to precisely define the metastable zone, enabling the predictive rescue of nucleation-limited systems. The synergy of these three strategies enables the systematic decoupling of nucleation from growth, providing a rational route to optimize microcrystal density, size and lattice order. Crucially, by eliminating the evaporation-related variables inherent in vapor diffusion, this method ensures that the chemical coordinates identified during screening remain constant during scale-up to larger volumes. This workflow transforms empirical serial crystallography sample preparation into a rational, reproducible and highly efficient process applicable to both the optimization of known conditions and the &lt;em&gt;de novo&lt;/em&gt; development of microcrystal suspensions, tailored to the rigorous demands of modern serial diffraction experiments.&lt;/div&gt;&lt;/","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 159-168"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146052325","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":"Enzyme therapy in a structural light","authors":"Jon Cooper","doi":"10.1107/S2052252526001557","DOIUrl":"10.1107/S2052252526001557","url":null,"abstract":"<div><div>The paper by Gilski <em>et al.</em> in this issue [<em>IUCrJ</em> (2026), <strong>13</strong>, 132–145] focuses on the stereochemical analysis of the catalytic mechanism of asparaginases with the aim of resolving key ambiguities in the mechanism. These enzymes have found truly remarkable therapeutic success in the treatment of childhood leukemias.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 2","pages":"Pages 126-127"},"PeriodicalIF":3.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147325729","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}