Pub Date : 2025-01-01DOI: 10.1107/S2052252524011060
Roman Gajda , Wojciech Sławiński , Tomasz Poręba , Jan Parafiniuk , Mohamed Mezouar , Przemysław Dera , Krzysztof Woźniak
Refinement of the hemimorphite crystal structure using single-crystal synchrotron X-ray diffraction data collected at high pressure revealed a structural phase transition into an incommensurately modulated structure, accompanied by the appearance of satellite reflections.
High-resolution single-crystal X-ray diffraction experiments on Zn4Si2O7(OH)2·H2O hemimorphite were conducted at high pressure using diamond anvil cells at several different synchrotron facilities (ESRF, Elettra, DESY). Experimental data confirmed the existence of a previously reported phase transition and revealed the exact nature of the incommensurate modulation. We report the incommensurately modulated structure described in the (3+1)D space group Pnn2(0, β, 0)000. We have determined the modulation mechanism, which involves the fluctuation of atoms between two main positions, occurring mainly along the [100] direction, perpendicular to the modulation vector. Moreover, our results reveal that the phase transition occurs at lower pressure than previously reported.
{"title":"Incommensurately modulated structure of Zn4Si2O7(OH)2·H2O at high pressure","authors":"Roman Gajda , Wojciech Sławiński , Tomasz Poręba , Jan Parafiniuk , Mohamed Mezouar , Przemysław Dera , Krzysztof Woźniak","doi":"10.1107/S2052252524011060","DOIUrl":"10.1107/S2052252524011060","url":null,"abstract":"<div><div>Refinement of the hemimorphite crystal structure using single-crystal synchrotron X-ray diffraction data collected at high pressure revealed a structural phase transition into an incommensurately modulated structure, accompanied by the appearance of satellite reflections.</div></div><div><div>High-resolution single-crystal X-ray diffraction experiments on Zn<sub>4</sub>Si<sub>2</sub>O<sub>7</sub>(OH)<sub>2</sub>·H<sub>2</sub>O hemimorphite were conducted at high pressure using diamond anvil cells at several different synchrotron facilities (ESRF, Elettra, DESY). Experimental data confirmed the existence of a previously reported phase transition and revealed the exact nature of the incommensurate modulation. We report the incommensurately modulated structure described in the (3+1)D space group <em>Pnn</em>2(0, β, 0)000. We have determined the modulation mechanism, which involves the fluctuation of atoms between two main positions, occurring mainly along the [100] direction, perpendicular to the modulation vector. Moreover, our results reveal that the phase transition occurs at lower pressure than previously reported.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 62-73"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739133","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}
Pub Date : 2025-01-01DOI: 10.1107/S2052252524012478
María Guadalupe Vasquez-Ríos
In the recent publication by Zhou et al. [(2025). IUCrJ, 12, 16–22], the crystal structure of benzo[a]pyrene was studied under high pressure up to 28 GPa using single-crystal X-ray diffraction and DFT calculations. This commentary highlights the importance of high pressure for analyzing organic molecular crystals.
{"title":"Using high pressure to understand the behavior of organic molecular crystals","authors":"María Guadalupe Vasquez-Ríos","doi":"10.1107/S2052252524012478","DOIUrl":"10.1107/S2052252524012478","url":null,"abstract":"<div><div>In the recent publication by Zhou <em>et al.</em> [(2025). <em>IUCrJ</em>, <strong>12</strong>, 16–22], the crystal structure of benzo[<em>a</em>]pyrene was studied under high pressure up to 28 GPa using single-crystal X-ray diffraction and DFT calculations. This commentary highlights the importance of high pressure for analyzing organic molecular crystals.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 4-5"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931635","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}
Pub Date : 2025-01-01DOI: 10.1107/S2052252524011242
Michał Chodkiewicz , Krzysztof Woźniak
We demonstrate that applying the alternative electron density partition in a Hirshfeld atom refinement may significantly improve the accuracy of hydrogen atom parameters. The new partition leads to less overlapping atomic densities. As a result, hydrogen atom parameters are less dependent on the structural parameters of their neighbours and their inaccuracies.
Hirshfeld atom refinement (HAR) is generally the chosen method for obtaining accurate hydrogen atom parameters from X-ray diffraction data. Still, determination can prove challenging, especially in the case of atomic displacement parameters (ADPs). We demonstrate that such a situation can occur when the ADP values of the bonding partner of the hydrogen atom are not determined accurately. Atomic electron densities partially overlap and inaccuracies in the bonding neighbour ADPs can be partially compensated for with modifications to the hydrogen ADPs. We introduce a modified version of the original Hirshfeld partition: the exponential Hirshfeld partition, parameterized with an adjustable parameter (n) to allow control of the overlap level of the atomic electron densities which, for n = 1, is equivalent to the Hirshfeld partition. The accuracy of the HAR-like procedure using the new partition (expHAR) was tested on a set of organic structures using B3LYP and MP2 electron densities. Applying expHAR improved the hydrogen atom parameters in the majority of the structures (compared with HAR), especially in cases with the highest deviations from the reference neutron values. X—H bond lengths and hydrogen ADPs improved for 9/10 of the structures for B3LYP-based refinement and 8/9 for MP2-based refinement when the ADPs were compared with a newly introduced scale-independent similarity measure.
{"title":"Towards improved accuracy of Hirshfeld atom refinement with an alternative electron density partition","authors":"Michał Chodkiewicz , Krzysztof Woźniak","doi":"10.1107/S2052252524011242","DOIUrl":"10.1107/S2052252524011242","url":null,"abstract":"<div><div>We demonstrate that applying the alternative electron density partition in a Hirshfeld atom refinement may significantly improve the accuracy of hydrogen atom parameters. The new partition leads to less overlapping atomic densities. As a result, hydrogen atom parameters are less dependent on the structural parameters of their neighbours and their inaccuracies.</div></div><div><div>Hirshfeld atom refinement (HAR) is generally the chosen method for obtaining accurate hydrogen atom parameters from X-ray diffraction data. Still, determination can prove challenging, especially in the case of atomic displacement parameters (ADPs). We demonstrate that such a situation can occur when the ADP values of the bonding partner of the hydrogen atom are not determined accurately. Atomic electron densities partially overlap and inaccuracies in the bonding neighbour ADPs can be partially compensated for with modifications to the hydrogen ADPs. We introduce a modified version of the original Hirshfeld partition: the exponential Hirshfeld partition, parameterized with an adjustable parameter (<em>n</em>) to allow control of the overlap level of the atomic electron densities which, for <em>n</em> = 1, is equivalent to the Hirshfeld partition. The accuracy of the HAR-like procedure using the new partition (expHAR) was tested on a set of organic structures using B3LYP and MP2 electron densities. Applying expHAR improved the hydrogen atom parameters in the majority of the structures (compared with HAR), especially in cases with the highest deviations from the reference neutron values. <em>X</em>—H bond lengths and hydrogen ADPs improved for 9/10 of the structures for B3LYP-based refinement and 8/9 for MP2-based refinement when the ADPs were compared with a newly introduced scale-independent similarity measure.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 74-87"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854286","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}
Pub Date : 2025-01-01DOI: 10.1107/S2052252524011734
Ewa Patyk-Kaźmierczak , Kornelia Szymańska , Michał Kaźmierczak
The negative linear compressibility and negative thermal expansion behaviours of two isostructural 1:1 cocrystals of 1,2-bis(4′-pyridyl)ethane with fumaric and succinic acids were revealed and compared, showing surprisingly strong ramifications of a small steric hindrance on the magnitude of both effects.
Multicomponent crystals have great scientific potential because of their amenability to crystal engineering in terms of composition and structure, and hence their properties can be easily modified. More and more research areas are employing the design of multicomponent materials to improve the known or induce novel physicochemical properties of crystals, and recently they have been explored as materials with abnormal pressure behaviour. The cocrystal of 1,2-bis(4′-pyridyl)ethane and fumaric acid (ETYFUM) exhibits a negative linear compressibility behaviour comparable to that of framework and metal-containing materials, but overcomes many of their deficiencies restricting their use. Herein ETYFUM was investigated at low temperature to reveal negative thermal expansion behaviour. Additionally, a cocrystal isostructural with ETYFUM, based on 1,2-bis(4′-pyridyl)ethane and succinic acid (ETYSUC), was exposed to high pressure and low temperature, showing that its behaviour is similar in nature to that of ETYFUM, but significantly differs in the magnitude of both effects. It was revealed that the minor structural difference between the acid molecules does not significantly affect the packing under ambient conditions, but has far-reaching consequences when it comes to the deformation of the structure when exposed to external stimuli.
{"title":"Managing negative linear compressibility and thermal expansion through steric hindrance: a case study of 1,2-bis(4′-pyridyl)ethane cocrystals","authors":"Ewa Patyk-Kaźmierczak , Kornelia Szymańska , Michał Kaźmierczak","doi":"10.1107/S2052252524011734","DOIUrl":"10.1107/S2052252524011734","url":null,"abstract":"<div><div>The negative linear compressibility and negative thermal expansion behaviours of two isostructural 1:1 cocrystals of 1,2-bis(4′-pyridyl)ethane with fumaric and succinic acids were revealed and compared, showing surprisingly strong ramifications of a small steric hindrance on the magnitude of both effects.</div></div><div><div>Multicomponent crystals have great scientific potential because of their amenability to crystal engineering in terms of composition and structure, and hence their properties can be easily modified. More and more research areas are employing the design of multicomponent materials to improve the known or induce novel physicochemical properties of crystals, and recently they have been explored as materials with abnormal pressure behaviour. The cocrystal of 1,2-bis(4′-pyridyl)ethane and fumaric acid (ETYFUM) exhibits a negative linear compressibility behaviour comparable to that of framework and metal-containing materials, but overcomes many of their deficiencies restricting their use. Herein ETYFUM was investigated at low temperature to reveal negative thermal expansion behaviour. Additionally, a cocrystal isostructural with ETYFUM, based on 1,2-bis(4′-pyridyl)ethane and succinic acid (ETYSUC), was exposed to high pressure and low temperature, showing that its behaviour is similar in nature to that of ETYFUM, but significantly differs in the magnitude of both effects. It was revealed that the minor structural difference between the acid molecules does not significantly affect the packing under ambient conditions, but has far-reaching consequences when it comes to the deformation of the structure when exposed to external stimuli.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 88-96"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864193","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}
Pub Date : 2025-01-01DOI: 10.1107/S2052252524011941
B. M. Murphy , A. Götz , C. Gutt , C. McGuinness , H. M. Rønnow , A. Schneidewind , S. Deledda , U. Pietsch
The German project DAPHNE4NFDI together with the European Synchrotron and Free Electron Laser User Organization (ESUO), the European Neutron Scattering Association (ENSA), and European synchrotron and neutron facilities continue the development of FAIR data handling procedures laid out by the EU-funded projects PaNOSC and ExPaNDS. Written by members of these organizations, this ‘white paper’ documents the current status of this discussion.
The topic of data storage, traceability, and data use and reuse in the years following experiments is becoming an important topic in Europe and across the world. Many scientific communities are striving to create open data by the FAIR principles. This is a requirement from the European Commission for EU-funded projects and experiments at EU-funded research infrastructures (RIs) and from many national funding agencies. This is challenging for users of large-scale RIs such as neutron, photon, synchrotron and free-electron laser facilities. Users of photon and neutron (PaN) RIs employ a wide range of scattering, imaging and spectroscopic methods investigating the behaviour of matter with a broad scientific base across physics, chemistry and biology, including engineering, environmental, cultural heritage and medical applications. They produce large data volumes of up to 1 PByte per day in some cases. To ensure all these data are FAIR requires an enormous effort from PaN RIs. It requires not only the expansion of data storage capacity, but also the development and deployment of software for effective data storage, metadata schemes and implementation of effective data pipelines at each individual experiment across RIs. FAIR data also affect the carbon footprint related to large amounts of data and raise questions related to user authentication, rights of access and cyber security. The RIs alone cannot achieve such a transformational process. For successful open science, cooperation of the user communities is essential as they need to create and utilize existing tools to deliver FAIR data. In this white paper, the European PaN community outline and discuss the role and responsibilities of the users and RIs and their common accountability to achieve FAIR data. This paper shall serve as a starting point for a common user and RI approach on the European scale to achieve FAIR data.
{"title":"FAIR data – the photon and neutron communities move together towards open science","authors":"B. M. Murphy , A. Götz , C. Gutt , C. McGuinness , H. M. Rønnow , A. Schneidewind , S. Deledda , U. Pietsch","doi":"10.1107/S2052252524011941","DOIUrl":"10.1107/S2052252524011941","url":null,"abstract":"<div><div>The German project DAPHNE4NFDI together with the European Synchrotron and Free Electron Laser User Organization (ESUO), the European Neutron Scattering Association (ENSA), and European synchrotron and neutron facilities continue the development of FAIR data handling procedures laid out by the EU-funded projects PaNOSC and ExPaNDS. Written by members of these organizations, this ‘white paper’ documents the current status of this discussion.</div></div><div><div>The topic of data storage, traceability, and data use and reuse in the years following experiments is becoming an important topic in Europe and across the world. Many scientific communities are striving to create open data by the FAIR principles. This is a requirement from the European Commission for EU-funded projects and experiments at EU-funded research infrastructures (RIs) and from many national funding agencies. This is challenging for users of large-scale RIs such as neutron, photon, synchrotron and free-electron laser facilities. Users of photon and neutron (PaN) RIs employ a wide range of scattering, imaging and spectroscopic methods investigating the behaviour of matter with a broad scientific base across physics, chemistry and biology, including engineering, environmental, cultural heritage and medical applications. They produce large data volumes of up to 1 PByte per day in some cases. To ensure all these data are FAIR requires an enormous effort from PaN RIs. It requires not only the expansion of data storage capacity, but also the development and deployment of software for effective data storage, metadata schemes and implementation of effective data pipelines at each individual experiment across RIs. FAIR data also affect the carbon footprint related to large amounts of data and raise questions related to user authentication, rights of access and cyber security. The RIs alone cannot achieve such a transformational process. For successful open science, cooperation of the user communities is essential as they need to create and utilize existing tools to deliver FAIR data. In this white paper, the European PaN community outline and discuss the role and responsibilities of the users and RIs and their common accountability to achieve FAIR data. This paper shall serve as a starting point for a common user and RI approach on the European scale to achieve FAIR data.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 8-15"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914802","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}
Pub Date : 2024-11-01DOI: 10.1107/S2052252524008406
Kristoffer J. M. Lundgren , Octav Caldararu , Esko Oksanen , Ulf Ryde
We present a new implementation of quantum refinement interfacing the widely used Phenix and ORCA software. We show applications on a neutron structure of Mn superoxide dismutase, X-ray structures of V- and Fe-nitrogenase and a cryo-EM structure of particulate methane monooxygenase.
X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software Phenix and the freely available quantum mechanical software ORCA. Through application to manganese superoxide dismutase and V- and Fe-nitrogenase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.
X 射线和中子晶体学以及低温电子显微镜（cryo-EM）是获得生物大分子原子结构的最常用方法。它们的一个共同特点是，在典型分辨率下，实验数据需要辅以经验约束，以确保最终结构在化学上是合理的。对于氨基酸和核酸来说，这些约束条件是准确的，但对于底物、抑制剂、小分子配体和金属位点来说，往往就不那么准确了。这可以通过量子力学计算结构中一小部分有趣的部分来解决。这种方法被称为 "量子细化"（quantum refinement），已被证明可以局部改进结构，确定配体和金属的质子化和氧化态，并区分对结构的不同解释。在这里，我们介绍了一种新的量子细化实现方法，它将广泛使用的结构细化软件 Phenix 与免费提供的量子力学软件 ORCA 相结合。通过对锰超氧化物歧化酶、V-和F-氮化酶的应用，我们展示了该方法对 X 射线和中子晶体结构的有效作用，旧的结果可以重现，并且可以进行结构判别。我们讨论了如何选择实验数据和经验约束之间的权重系数，以及如何计算应变能等量子力学质量度量。我们还介绍了量子细化在微粒甲烷单加氧酶低温电子显微镜数据中的应用，并表明这可能是此类结构中金属位点的首选方法，因为目前还没有针对金属的精确经验约束。
{"title":"Quantum refinement in real and reciprocal space using the Phenix and ORCA software","authors":"Kristoffer J. M. Lundgren , Octav Caldararu , Esko Oksanen , Ulf Ryde","doi":"10.1107/S2052252524008406","DOIUrl":"10.1107/S2052252524008406","url":null,"abstract":"<div><div>We present a new implementation of quantum refinement interfacing the widely used <em>Phenix</em> and <em>ORCA</em> software. We show applications on a neutron structure of Mn superoxide dismutase, X-ray structures of V- and Fe-nitrogenase and a cryo-EM structure of particulate methane monooxygenase.</div></div><div><div>X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software <em>Phenix</em> and the freely available quantum mechanical software <em>ORCA</em>. Through application to manganese superoxide dismutase and V- and Fe-nitrogenase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 921-937"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347053","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}
Pub Date : 2024-11-01DOI: 10.1107/S2052252524009114
Filomeno Sánchez Rodríguez , Adam J. Simpkin , Grzegorz Chojnowski , Ronan M. Keegan , Daniel J. Rigden
A novel structure-validation method is applied to PDB depositions at 3–5 Å resolution, revealing large numbers of putative register errors.
The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, especially where the experimental data are of limited resolution. A novel protein structure validation approach based on spotting inconsistencies between the residue contacts and distances observed in a structural model and those computationally predicted by methods such as AlphaFold2 has previously been established. It is particularly well suited to the detection of register errors. Importantly, this new approach is orthogonal to traditional methods based on stereochemistry or map–model agreement, and is resolution independent. Here, thousands of likely register errors are identified by scanning 3–5 Å resolution structures in the PDB. Unlike most methods, the application of this approach yields suggested corrections to the register of affected regions, which it is shown, even by limited implementation, lead to improved refinement statistics in the vast majority of cases. A few limitations and confounding factors such as fold-switching proteins are characterized, but this approach is expected to have broad application in spotting potential issues in current accessions and, through its implementation and distribution in CCP4, helping to ensure the accuracy of future depositions.
蛋白质数据库（PDB）中信息的准确性对于利用蛋白质结构信息的无数下游应用来说非常重要。尽管已经尽了最大努力，但偶尔引入误差是不可避免的，尤其是在实验数据分辨率有限的情况下。一种新颖的蛋白质结构验证方法基于发现结构模型中观察到的残基接触和距离与 AlphaFold2 等方法计算预测的残基接触和距离之间的不一致。这种方法尤其适用于检测寄存器错误。重要的是，这种新方法与基于立体化学或图谱-模型一致性的传统方法是正交的，并且与分辨率无关。在这里，通过扫描 PDB 中 3-5 Å 分辨率的结构，可以识别出数千个可能的套准错误。与大多数方法不同的是，应用这种方法会对受影响区域的配准产生建议性修正，即使实施有限，也能在绝大多数情况下改善精炼统计。虽然存在一些局限性和混杂因素（如折叠转换蛋白），但这种方法有望广泛应用于发现当前入库中的潜在问题，并通过其在 CCP4 中的实施和传播，帮助确保未来入库的准确性。
{"title":"Using deep-learning predictions reveals a large number of register errors in PDB depositions","authors":"Filomeno Sánchez Rodríguez , Adam J. Simpkin , Grzegorz Chojnowski , Ronan M. Keegan , Daniel J. Rigden","doi":"10.1107/S2052252524009114","DOIUrl":"10.1107/S2052252524009114","url":null,"abstract":"<div><div>A novel structure-validation method is applied to PDB depositions at 3–5 Å resolution, revealing large numbers of putative register errors.</div></div><div><div>The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, especially where the experimental data are of limited resolution. A novel protein structure validation approach based on spotting inconsistencies between the residue contacts and distances observed in a structural model and those computationally predicted by methods such as <em>AlphaFold</em>2 has previously been established. It is particularly well suited to the detection of register errors. Importantly, this new approach is orthogonal to traditional methods based on stereochemistry or map–model agreement, and is resolution independent. Here, thousands of likely register errors are identified by scanning 3–5 Å resolution structures in the PDB. Unlike most methods, the application of this approach yields suggested corrections to the register of affected regions, which it is shown, even by limited implementation, lead to improved refinement statistics in the vast majority of cases. A few limitations and confounding factors such as fold-switching proteins are characterized, but this approach is expected to have broad application in spotting potential issues in current accessions and, through its implementation and distribution in <em>CCP</em>4, helping to ensure the accuracy of future depositions.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 938-950"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142465949","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}
Pub Date : 2024-11-01DOI: 10.1107/S2052252524009722
Muchammad Izzuddin Jundullah Hanafi , Lorenzo Bastonero , Mohammad Mangir Murshed , Lars Robben , Wilke Dononelli , Andrea Kirsch , Nicola Marzari , Thorsten M. Gesing
Ball milling of forsterite (Mg2SiO4) was carried out to mimic mechanical weathering processes on Mars. The defective forsterite structure models, capable of describing both long-range and short-range order, are deduced by density functional theory assisted pair distribution function analysis.
Regolith draws intensive research attention because of its importance as the basis for fabricating materials for future human space exploration. Martian regolith is predicted to consist of defect-rich crystal structures due to long-term space weathering. The present report focuses on the structural differences between defect-rich and defect-poor forsterite (Mg2SiO4) – one of the major phases in Martian regolith. In this work, forsterites were synthesized using reverse strike co-precipitation and high-energy ball milling (BM). Subsequent post-processing was also carried out using BM to enhance the defects. The crystal structures of the samples were characterized by X-ray powder diffraction and total scattering using Cu and synchrotron radiation followed by Rietveld refinement and pair distribution function (PDF) analysis, respectively. The structural models were deduced by density functional theory assisted PDF refinements, describing both long-range and short-range order caused by defects. The Raman spectral features of the synthetic forsterites complement the ab initio simulation for an in-depth understanding of the associated structural defects.
火星岩石是制造未来人类太空探索所需材料的重要基础，因此吸引了大量研究人员的关注。据预测，由于长期的空间风化，火星摄岩石由富含缺陷的晶体结构组成。本报告的重点是火星残留岩中的主要物相之一--富缺陷和贫缺陷绿柱石（Mg2SiO4）之间的结构差异。在这项工作中，采用反向打击共沉淀和高能球磨（BM）技术合成了福斯特岩。随后还使用球磨进行了后处理，以强化缺陷。利用铜和同步辐射的 X 射线粉末衍射和全散射对样品的晶体结构进行了表征，然后分别进行了里特维尔德细化和配对分布函数（PDF）分析。通过密度泛函理论辅助的 PDF 精炼推导出了结构模型，描述了缺陷引起的长程和短程有序。合成硼酸盐的拉曼光谱特征与 ab initio 模拟相辅相成，有助于深入了解相关的结构缺陷。
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Pub Date : 2024-11-01DOI: 10.1107/S2052252524010170
Sofia M. Kapetanaki , Nicolas Coquelle , David von Stetten , Martin Byrdin , Ronald Rios-Santacruz , Richard Bean , Johan Bielecki , Mohamed Boudjelida , Zsuzsana Fekete , Geoffrey W. Grime , Huijong Han , Caitlin Hatton , Sravya Kantamneni , Konstantin Kharitonov , Chan Kim , Marco Kloos , Faisal H. M. Koua , Iñaki de Diego Martinez , Diogo Melo , Lukas Rane , Martin Weik
Structures of the dark-adapted state of a photoactivated adenylate cyclase were determined from serial crystallography (SX) data collected at room temperature at an X-ray free-electron laser and a synchrotron, and are compared with cryo-macromolecular crystallography (MX) synchrotron structures obtained by us and others. These structures of the wild-type enzyme in combination with the cryo-MX synchrotron structure of a light-sensor domain mutant provide insight into the hydrogen-bond network rearrangement upon blue-light illumination and pave the way for the determination of structural intermediates of the enzyme by time-resolved SX.
OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates.
OaPAC 是最近发现的一种利用蓝光的黄素腺苷二核苷酸（BLUF）光活化腺苷酸环化酶，它来自蓝藻 Oscillatoria acuminata，利用三磷酸腺苷并将光信号转化为环状单磷酸腺苷的产生。在此，我们报告了该酶在无天然底物情况下的晶体结构，这些晶体结构是根据在 X 射线自由电子激光器和同步加速器上收集的室温序列晶体学数据确定的，我们还将这些结构与我们和其他人在同步加速器上获得的低温大分子晶体学结构进行了比较。这些结果表明，由于在不同温度和 X 射线源下采集的数据不同，酶的结构也略有差异。我们进一步研究了 BLUF 结构域中 Y6W 突变的影响，该突变导致黄素周围氢键网络的重新排列以及关键 Gln48 残基侧链的显著旋转。这些研究为在 X 射线自由电子激光器和同步加速器上进行皮秒-毫微秒时间分辨序列晶体学实验铺平了道路，以便确定早期的结构中间产物，并将它们与研究得很好的皮秒-毫微秒光谱中间产物联系起来。
{"title":"Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography","authors":"Sofia M. Kapetanaki , Nicolas Coquelle , David von Stetten , Martin Byrdin , Ronald Rios-Santacruz , Richard Bean , Johan Bielecki , Mohamed Boudjelida , Zsuzsana Fekete , Geoffrey W. Grime , Huijong Han , Caitlin Hatton , Sravya Kantamneni , Konstantin Kharitonov , Chan Kim , Marco Kloos , Faisal H. M. Koua , Iñaki de Diego Martinez , Diogo Melo , Lukas Rane , Martin Weik","doi":"10.1107/S2052252524010170","DOIUrl":"10.1107/S2052252524010170","url":null,"abstract":"<div><div>Structures of the dark-adapted state of a photoactivated adenylate cyclase were determined from serial crystallography (SX) data collected at room temperature at an X-ray free-electron laser and a synchrotron, and are compared with cryo-macromolecular crystallography (MX) synchrotron structures obtained by us and others. These structures of the wild-type enzyme in combination with the cryo-MX synchrotron structure of a light-sensor domain mutant provide insight into the hydrogen-bond network rearrangement upon blue-light illumination and pave the way for the determination of structural intermediates of the enzyme by time-resolved SX.</div></div><div><div>OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium <em>Oscillatoria acuminata</em> that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 991-1006"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521897","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}
Pub Date : 2024-11-01DOI: 10.1107/S2052252524008583
Madeleine Geers , Oscar Fabelo , Matthew J. Cliffe , Laura Cañadillas-Delgado
We show that the modulated phase transitions in solid solutions of [CH3NH3]CoxNi1−x(HCOO)3, with x = 0.25 (1), x = 0.50 (2) and x = 0.75 (3), can be tuned by the metal ratio, which offers the opportunity to consciously build molecular compounds with adjustable properties by doping metal sites.
Three solid solutions of [CH3NH3]CoxNi1−x(HCOO)3, with x = 0.25 (1), x = 0.50 (2) and x = 0.75 (3), were synthesized and their nuclear structures and magnetic properties were characterized using single-crystal neutron diffraction and magnetization measurements. At room temperature, all three compounds crystallize in the Pnma orthorhombic space group, akin to the cobalt and nickel end series members. On cooling, each compound undergoes a distinct series of structural transitions to modulated structures. Compound 1 exhibits a phase transition to a modulated structure analogous to the pure Ni compound [Cañadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodríguez-Carvajal, J. & Petricek, V. (2020). Inorg. Chem.59, 17896–17905], whereas compound 3 maintains the behaviour observed in the pure Co compound reported previously [Canadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodriguez-Velamazan, J. A. & Rodriguez-Carvajal, J. (2019). IUCrJ, 6, 105–115], although in both cases the temperatures at which the phase transitions occur differ slightly from the pure phases. Monochromatic neutron diffraction measurements showed that the structural evolution of 2 diverges from that of either parent compound, with competing hydrogen bond interactions that drive the modulation throughout the series, producing a unique sequence of phases. It involves two modulated phases below 96 (3) and 59 (3) K, with different q vectors, similar to the pure Co compound (with modulated phases below 128 and 96 K); however, it maintains the modulated phase below magnetic order [at 22.5 (7) K], resembling the pure Ni compound (which presents magnetic order below 34 K), resulting in an improper modulated magnetic structure. Despite these large-scale structural changes, magnetometry data reveal that the bulk magnetic properties of these solid solutions form a linear continuum between the end members. Notably, doping of the metal site in these solid solutions allows for tuning of bulk magnetic properties, including magnetic ordering temperature, transition temperatures and the nature of nuclear phase transitions, through adjustment of metal ratios.
我们合成了三种 [CH3NH3]CoxNi1-x(HCOO)3 固溶体（x = 0.25 (1)、x = 0.50 (2) 和 x = 0.75 (3)），并利用单晶中子衍射和磁化测量对它们的核结构和磁性能进行了表征。在室温下，这三种化合物都在 Pnma 正交空间群中结晶，类似于钴和镍端系列成员。冷却时，每种化合物都会经历一系列不同的结构转变，形成调制结构。化合物 1 显示了向类似于纯镍化合物的调制结构的相变[Cañadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodríguez-Carvajal, J. & Petricek, V. (2020)。Inorg.Chem.59，17896-17905]，而化合物 3 保持了之前报告的纯 Co 化合物中观察到的行为[Canadillas-Delgado，L.，Mazzuca，L.，Fabelo，O.，Rodriguez-Velamazan，J. A. & Rodriguez-Carvajal, J. (2019)。IUCrJ, 6, 105-115]，尽管在这两种情况下发生相变的温度与纯相略有不同。单色中子衍射测量结果表明，2 的结构演化与母体化合物的结构演化不同，竞争性氢键相互作用推动了整个系列的调制，产生了独特的相序列。它在 96 (3) K 和 59 (3) K 以下涉及两个调制相，具有不同的 q 向量，与纯 Co 化合物类似（在 128 K 和 96 K 以下具有调制相）；然而，它在磁序[22.5 (7) K]以下保持调制相，与纯 Ni 化合物类似（在 34 K 以下呈现磁序），从而产生了不恰当的调制磁结构。尽管存在这些大规模的结构变化，但磁力测量数据显示，这些固溶体的体磁性能在末端成员之间形成了一个线性连续体。值得注意的是，在这些固溶体中掺杂金属位点可以通过调整金属比例来调整体磁特性，包括磁有序温度、转变温度和核相变的性质。
{"title":"Tuning structural modulation and magnetic properties in metal–organic coordination polymers [CH3NH3]CoxNi1−x(HCOO)3","authors":"Madeleine Geers , Oscar Fabelo , Matthew J. Cliffe , Laura Cañadillas-Delgado","doi":"10.1107/S2052252524008583","DOIUrl":"10.1107/S2052252524008583","url":null,"abstract":"<div><div>We show that the modulated phase transitions in solid solutions of [CH<sub>3</sub>NH<sub>3</sub>]Co<sub><em>x</em></sub>Ni<sub>1−<em>x</em></sub>(HCOO)<sub>3</sub>, with <em>x</em> = 0.25 (<strong>1</strong>), <em>x</em> = 0.50 (<strong>2</strong>) and <em>x</em> = 0.75 (<strong>3</strong>), can be tuned by the metal ratio, which offers the opportunity to consciously build molecular compounds with adjustable properties by doping metal sites.</div></div><div><div>Three solid solutions of [CH<sub>3</sub>NH<sub>3</sub>]Co<em><sub>x</sub></em>Ni<sub>1−<em>x</em></sub>(HCOO)<sub>3</sub>, with <em>x</em> = 0.25 (<strong>1</strong>), <em>x</em> = 0.50 (<strong>2</strong>) and <em>x</em> = 0.75 (<strong>3</strong>), were synthesized and their nuclear structures and magnetic properties were characterized using single-crystal neutron diffraction and magnetization measurements. At room temperature, all three compounds crystallize in the <em>Pnma</em> orthorhombic space group, akin to the cobalt and nickel end series members. On cooling, each compound undergoes a distinct series of structural transitions to modulated structures. Compound <strong>1</strong> exhibits a phase transition to a modulated structure analogous to the pure Ni compound [Cañadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodríguez-Carvajal, J. & Petricek, V. (2020). <em>Inorg. Chem.</em><strong>59</strong>, 17896–17905], whereas compound <strong>3</strong> maintains the behaviour observed in the pure Co compound reported previously [Canadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodriguez-Velamazan, J. A. & Rodriguez-Carvajal, J. (2019). <em>IUCrJ</em>, <strong>6</strong>, 105–115], although in both cases the temperatures at which the phase transitions occur differ slightly from the pure phases. Monochromatic neutron diffraction measurements showed that the structural evolution of <strong>2</strong> diverges from that of either parent compound, with competing hydrogen bond interactions that drive the modulation throughout the series, producing a unique sequence of phases. It involves two modulated phases below 96 (3) and 59 (3) K, with different <strong>q</strong> vectors, similar to the pure Co compound (with modulated phases below 128 and 96 K); however, it maintains the modulated phase below magnetic order [at 22.5 (7) K], resembling the pure Ni compound (which presents magnetic order below 34 K), resulting in an improper modulated magnetic structure. Despite these large-scale structural changes, magnetometry data reveal that the bulk magnetic properties of these solid solutions form a linear continuum between the end members. Notably, doping of the metal site in these solid solutions allows for tuning of bulk magnetic properties, including magnetic ordering temperature, transition temperatures and the nature of nuclear phase transitions, through adjustment of metal ratios.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 910-920"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307792","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}
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