IUCrJ最新文献

{"title":"Using multiple computer-predicted structures as molecular replacement models: application to the antiviral mini-protein LCB2.","authors":"Svetlana A Korban, Oleg Mikhailovskii, Vladislav V Gurzhiy, Ivan S Podkorytov, Nikolai R Skrynnikov","doi":"10.1107/S2052252525005123","DOIUrl":"10.1107/S2052252525005123","url":null,"abstract":"<p><p>In this report, we describe a set of structures of the engineered protein LCB2 that has been solved starting from different computer-predicted molecular replacement (MR) models. We found that AlphaFold3, AlphaFold2, MultiFOLD, Rosetta, RoseTTAFold and trRosetta all produced successful MR models for this three-helix bundle 58-residue protein, while some of the older predictors failed. To assign B factors in the MR models we used the predictor-generated confidence scores or, as a convenient alternative, the accessible surface area (ASA) values. The process of multi-start structure determination using Coot and Phenix demonstrated good convergence, leading to six structures within 0.25 Å (all-atom RMSD) of each other. Of note, structural differences between the computer-predicted MR models and the final structures can be largely attributed to a single specific crystal contact. Comparing the six structural solutions, we observe that a number of surface side chains have been solved with different conformations. Interestingly, for each individual structure the electron density is consistent with a single rotameric state and offers no direct evidence of conformational heterogeneity. Strictly speaking, this behavior constitutes a case of model bias; we argue, however, that it represents a benign side of model bias. Specifically, when we use a model where the side-chain conformation corresponds to one of the actual (significantly populated) rotameric states, this leads to an enhancement of the electron density for this particular conformation. Conversely, when we use a model with an irrelevant (low-population) side-chain conformation, it fails to produce the matching electron density. We thus conclude that the six LCB2 structures obtained in this study can be grouped into a multiconformer ensemble, where structural variations are representative of protein's conformational dynamics. Indeed, using this six-member ensemble leads to a significant drop in R_work and R_free compared with the individual solutions. This interpretation was also supported by our MD simulations of the LCB2 crystal.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"488-501"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475326","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":"High-resolution synchrotron X-ray study of icosahedrite, an icosahedral AlCuFe quasicrystal from the Khatyrka meteorite.","authors":"H Takakura, K Mizunuma, T Yamada, A Bosak, F Formisano, L Paolasini, M de Boissieu, P J Steinhardt, L Bindi","doi":"10.1107/S2052252525004130","DOIUrl":"10.1107/S2052252525004130","url":null,"abstract":"<p><p>Icosahedrite, natural icosahedral Al₆₃Cu₂₄Fe₁₃, was discovered in a meteorite about 15 years ago. We have carried out a high-resolution X-ray diffraction study on a sample of this meteoritic mineral at the ESRF. The diffraction pattern turned out to be identical to an intermediate phase observed in synthetic i-AlCuFe during the transformation from the quasicrystalline state to a periodic rhombohedral phase. This particular natural Al₆₃Cu₂₄Fe₁₃ grain is an icosahedral quasicrystal on which a modulation by six cosine waves propagating along the fivefold axes is superimposed, with a wavelength of about 20 nm and a polarization in the phason/perpendicular space. By examining the thermodynamic conditions for producing this modulated icosahedral phase at high pressure in the laboratory, we may gain insights into the formation process of the Khatyrka meteorite.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"435-443"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127413","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":"Models of thermal motion in small-molecule crystallography.","authors":"Anna Hoser, Anders Ø Madsen","doi":"10.1107/S2052252525004361","DOIUrl":"10.1107/S2052252525004361","url":null,"abstract":"<p><p>The Debye-Waller factor, introduced a century ago, remains a fundamental component in the refinement of crystal structures against X-ray, neutron and electron diffraction data. This review marks its centenary by exploring its applications in small-molecule crystallography. We provide a historical overview of the development of the Debye-Waller factor and its foundations in lattice dynamics. The review discusses the practical use of anisotropic displacement parameters and their role in accurate structure determination. We also address the challenges and advancements in modelling thermal motion and disorder, the role of multi-temperature measurements and modern computational approaches.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"421-434"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234150","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":"Femtosecond X-ray cross-correlation analysis of disordered crystals forming in a supercooled atomic liquid.","authors":"Johannes Möller, Michele Caresana, Alexander Schottelius, Felix Lehmkühler, Ulrike Boesenberg, Frédéric Caupin, Francesco Dallari, Tiberio A Ezquerra, José M Fernández, Luca Gelisio, Claudia Goy, Jörg Hallmann, Anton Kalinin, Chan Kim, Ruslan P Kurta, Dmitry Lapkin, Francesco Mambretti, Markus Scholz, Roman Shayduk, René Steinbrügge, Florian Trinter, Ivan A Vartanyants, Alexey Zozulya, Davide E Galli, Gerhard Grübel, Anders Madsen, Robert E Grisenti","doi":"10.1107/S2052252525004063","DOIUrl":"10.1107/S2052252525004063","url":null,"abstract":"<p><p>We demonstrate an advanced scattering method for accessing the 3D reciprocal space of crystalline structures forming in a rapidly supercooled noble-gas liquid using a combination of femtosecond X-ray diffraction and X-ray cross-correlation analysis. The preservation of angular information from the scattering signal allows probing the structure factor along selected directions in reciprocal space and identifying signatures undetectable in azimuthally integrated scattering curves. Therefore, more information from serial diffraction experiments on stochastic crystallization processes can be retrieved despite the inherent variation of the crystal orientation and morphology for each single probe. We also demonstrate how different features in the correlation maps can be associated with certain forms of stacking faults, which enables studying such defects in situ and disentangling them from simultaneous changes in crystal size and temperature.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"462-471"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208606","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":"Everything you always wanted to know about the Debye-Waller factor but were afraid to ask.","authors":"Richard Dronskowski","doi":"10.1107/S2052252525004968","DOIUrl":"10.1107/S2052252525004968","url":null,"abstract":"<p><p>Combining improved diffraction methods, modeling approaches and advanced computations allows for a detailed understanding of atomic thermal motions in crystals. Thus, the Topical Review by Hoser & Madsen [(2025). IUCrJ 12, 421-434] covers the Debye-Waller factor, the importance of anisotropic displacement parameters, and the interplay of experiment and theory to accurately capture collective atomic vibrations in molecular crystals.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"417-418"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234149","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":"On the flexibility of the multipole model refinement. A DFT benchmark study of the tetrakis(μ-acetato)diaquadicopper model system.","authors":"Andrej Hlinčík, Tadeáš Fülöp, Peter Herich, Jozef Kožíšek, Karol Lušpai, Lukáš Bučinský","doi":"10.1107/S2052252525003355","DOIUrl":"10.1107/S2052252525003355","url":null,"abstract":"<p><p>In this study, the flexibility of the multipole Hansen-Coppens (HC) model refinement is investigated on calculated structure factors from a DFT reference for the tetrakis(μ-acetato)diaquadicopper model system (CCDC reference 1811668). The effect of the resolution [sin(θ)/λ], the Cu scattering factor, the inclusion of anisotropic displacement parameters and the positions of the atoms in the refinement are considered in terms of statistical error analysis, residual and deformation density maps, Atoms In Molecules parameters, d-orbital populations, and others. The choice of the neutral Cu scattering factor in the HC refinement is found to give the most satisfactory results for most of the monitored parameters, despite the formal Cu²⁺ nature of copper in the studied complex. In order to put the difference between the HC model and the reference DFT (BLYP functional) results on the right scale, several computational chemistry methods (B3LYP, Hartree-Fock, Møller-Plesset perturbation theory and Coupled Clusters Singles and Doubles) were compared with the chosen DFT reference. Differences in the magnitudes of the structure factors and AIM parameters are presented, including considerations of relativistic effects and periodic boundary conditions, i.e. a comparison of a molecular crystal calculation versus an isolated molecule in the crystal.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"444-461"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127485","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":"In situ high-resolution cryo-EM reconstructions from CEMOVIS.","authors":"Johannes Elferich, Marek Kaminek, Lingli Kong, Adolfo Odriozola, Wanda Kukulski, Benoît Zuber, Nikolaus Grigorieff","doi":"10.1107/S2052252525005196","DOIUrl":"10.1107/S2052252525005196","url":null,"abstract":"<p><p>Cryo-electron microscopy can be used to image cells and tissue at high resolution. To ensure electron transparency, the sample thickness must not exceed 500 nm. Focused-ion-beam (FIB) milling has become the standard method for preparing thin samples (lamellae); however, the material removed by the milling process is lost, the imageable area is usually limited to a few square micrometres and the surface layers sustain damage from the ion beam. We have examined cryo-electron microscopy of vitreous sections (CEMOVIS), a technique based on cutting thin sections with a knife, as an alternative to FIB milling. Vitreous sections also sustain damage, including compression, shearing and cracks. However, samples can be sectioned in series, producing many orders of magnitude more imageable area compared to lamellae, making CEMOVIS an alternative to FIB milling with distinct advantages. Using two-dimensional template matching on images of vitreous sections of Saccharomyces cerevisiae cells, we reconstructed the 60S ribosomal subunit at near-atomic resolution, demonstrating that, in many regions of the sections, the molecular structure of these subunits is largely intact, comparable to FIB-milled lamellae.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"502-510"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475315","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":"Femtosecond X-rays illuminate disordered states during the early stages of crystallization.","authors":"Akinobu Niozu","doi":"10.1107/S2052252525005706","DOIUrl":"10.1107/S2052252525005706","url":null,"abstract":"<p><p>Crystallization is a fundamental non-equilibrium process in materials science, yet its early transient states remain difficult to probe experimentally. Möller et al. [(2025). IUCrJ 12, 462-471] use femtosecond X-ray scattering and X-ray cross-correlation analysis to reveal the structural evolution of defect-containing crystals forming in a supercooled noble-gas liquid.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 Pt 4","pages":"419-420"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553618","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":"Benchmarking quantum chemical methods with X-ray structures via structure-specific restraints.","authors":"Birger Dittrich, Rok Breznikar, Gianluca Santarossa, Pamela Whitfield, Henrik Moebitz","doi":"10.1107/S2052252525004543","DOIUrl":"10.1107/S2052252525004543","url":null,"abstract":"<p><p>There is a need for fast, efficient and accurate solid-state structure optimization for imprecise crystal structures (`augmentation') for subsequent property prediction in the pharmaceutical industry. Crystal structures from single-crystal X-ray, 3D electron or powder diffraction are widely available but require augmentation to the same quality level for comparative studies. Properties can be best calculated when the level of theory is alike and the accuracy, as well as the precision, are high. Moreover, the size of molecules and the complexity of structures encountered in pharmaceutical research are increasing. Efficient procedures are thus required that can also treat structures with disorder and several molecules in the asymmetric unit of the unit cell. Hence, we investigated whether `molecule-in-cluster' (MIC) computations [Dittrich et al. (2020). CrystEngComm 22, 7420-7431] can reach the accuracy of full-periodic (FP) computations. Selected quantum mechanical methods are assessed. The evaluation criterion is how well the structures of 22 very low temperature high-quality structures are reproduced. Computational efficiency is also considered. A novel approach to evaluating the accuracy of quantum mechanical predictions is enforcing computed structure-specific restraints in crystallographic least-squares refinements. To complement this approach, root mean square Cartesian displacements of computed and experimental structures were also compared. Analysis shows that (a) MIC DFT-D computations in a quantum mechanics/molecular mechanics (QM:MM) framework provide improved restraints and coordinates over earlier MIC GFN2-xTB computations, (b) increasing QM basis-set size in MIC QM:MM does not systematically improve computations, and (c) the choice of DFT functional is less important than the choice of the basis set. Overall, MIC computations are an accurate and computationally efficient tool for solid-state structure optimization that can match FP computations to augment experimental structures.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"472-487"},"PeriodicalIF":2.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325752","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":"Damage before destruction? X-ray-induced changes in single-pulse serial femtosecond crystallography","authors":"Lewis J. Williams ,&nbsp;Amy J. Thompson ,&nbsp;Philipp Dijkstal ,&nbsp;Martin Appleby ,&nbsp;Greta Assmann ,&nbsp;Florian S. N. Dworkowski ,&nbsp;Nicole Hiller ,&nbsp;Chia-Ying Huang ,&nbsp;Tom Mason ,&nbsp;Samuel Perrett ,&nbsp;Eduard Prat ,&nbsp;Didier Voulot ,&nbsp;Bill Pedrini ,&nbsp;John H. Beale ,&nbsp;Michael A. Hough ,&nbsp;Jonathan A. R. Worrall ,&nbsp;Robin L. Owen","doi":"10.1107/S2052252525002660","DOIUrl":"10.1107/S2052252525002660","url":null,"abstract":"<div><div>Varied pulse-duration and pulse-intensity serial femtosecond crystallography data do not show significant signs of radiation damage under typical experimental conditions.</div></div><div><div>Serial femtosecond crystallography (SFX) exploits extremely brief X-ray free-electron laser pulses to obtain diffraction data before destruction of the crystal. However, during the pulse X-ray-induced site-specific radiation damage can occur, leading to electronic state and/or structural changes. Here, we present a systematic exploration of the effect of single-pulse duration and energy (and consequently different dose rates) on site-specific radiation damage under typical SFX room-temperature experimental conditions. For the first time in SFX we directly measured the photon pulse duration, varying from less than 10 fs to more than 50 fs, and used three pulse energies to probe in-pulse damage in two radiation-sensitive proteins: the iron-heme peroxidase DtpAa and the disulfide-rich thaumatin. While difference-map features arising from radiation damage are observed, they do not lead to significant change in refined atomic coordinates or key bond lengths. Our work thus provides experimental verification that average atomic coordinates are not significantly perturbed by radiation damage in typical SFX experiments.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 358-371"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902095","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}