Pub Date : 2023-07-07DOI: 10.1107/s2053273323098881
Peter W. Stephens, Rasika H. V. Dias, Andrey A. Yakovenko
Purification of ethylene from ethylene -ethane mixtures is an important and challenging industrial process, currently performed by highly energy-intensive cryogenic distillation. We have been studying the reversible reaction of C2H4 with various molecular pyrazolate complexes of copper, and fi nd that they are extremely selective for ethylene vs. ethane.1 -4 A typical gas-phase adsorption/desorption reaction, which occurs at 320 K – 343 K at atmospheric pressure, is illustrated in Fig. 1. We have performed in situ powder diffraction measurements of the repeated adsorption and desorption of ethylene from dense powders of several copper pyrazolate complexes at beamline 17 - BM of the Advanced Photon Source.2,3 We have determined previously unknown structures of several of the compounds and monitor the conversion between phases with and without adsorbed ethylene. It is truly remarkable that the subject molecules reversibly pass between trimer and dimer structures in the solid state upon reaction with ethylene.
{"title":"In situ studies of molecular copper compounds for highly selective purification of ethylene","authors":"Peter W. Stephens, Rasika H. V. Dias, Andrey A. Yakovenko","doi":"10.1107/s2053273323098881","DOIUrl":"https://doi.org/10.1107/s2053273323098881","url":null,"abstract":"Purification of ethylene from ethylene -ethane mixtures is an important and challenging industrial process, currently performed by highly energy-intensive cryogenic distillation. We have been studying the reversible reaction of C2H4 with various molecular pyrazolate complexes of copper, and fi nd that they are extremely selective for ethylene vs. ethane.1 -4 A typical gas-phase adsorption/desorption reaction, which occurs at 320 K – 343 K at atmospheric pressure, is illustrated in Fig. 1. We have performed in situ powder diffraction measurements of the repeated adsorption and desorption of ethylene from dense powders of several copper pyrazolate complexes at beamline 17 - BM of the Advanced Photon Source.2,3 We have determined previously unknown structures of several of the compounds and monitor the conversion between phases with and without adsorbed ethylene. It is truly remarkable that the subject molecules reversibly pass between trimer and dimer structures in the solid state upon reaction with ethylene.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323096304
Christopher J. Williams, Sushrit Pasumarthy, Jane S Richardson
Disulfide bridges between cysteine sidechains are one of the more unusual features of protein macromolecules. They provide a strong, stabilizing, covalent connection between sequence - distant parts of a protein. Previous efforts by the Richardson Lab to compile a comprehensive library of disulfide conformations were frustrated by our datasets being in sufficiently large in the face of the huge conformational space afforded by disulfides’ 5 chi torsions (more than lysine!). Now, enabled by the Top2018 dataset, we present our survey of disulfide bridges. Disulfides have great conformational diversity. This diversity is matched by the diversity of proteins and structural contexts they appear in. Nevertheless, disulfide conformations are often conserved among proteins with similar functions. Some conformations are even unique to certain protein families. Others are conserved according to their position relative to secondary structure. This library will aid in selection of appropriate disulfides in model building and in MolProbity-style validation of experimental and predicted models.
{"title":"A disulfide bridge survey and library","authors":"Christopher J. Williams, Sushrit Pasumarthy, Jane S Richardson","doi":"10.1107/s2053273323096304","DOIUrl":"https://doi.org/10.1107/s2053273323096304","url":null,"abstract":"Disulfide bridges between cysteine sidechains are one of the more unusual features of protein macromolecules. They provide a strong, stabilizing, covalent connection between sequence - distant parts of a protein. Previous efforts by the Richardson Lab to compile a comprehensive library of disulfide conformations were frustrated by our datasets being in sufficiently large in the face of the huge conformational space afforded by disulfides’ 5 chi torsions (more than lysine!). Now, enabled by the Top2018 dataset, we present our survey of disulfide bridges. Disulfides have great conformational diversity. This diversity is matched by the diversity of proteins and structural contexts they appear in. Nevertheless, disulfide conformations are often conserved among proteins with similar functions. Some conformations are even unique to certain protein families. Others are conserved according to their position relative to secondary structure. This library will aid in selection of appropriate disulfides in model building and in MolProbity-style validation of experimental and predicted models.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s205327332309928x
Gabrielle R. Budziszewski, Tiffany R. Wright, M. E. Snell, Miranda L. Lynch, Sarah E J Bowman
{"title":"Operations of the National Crystallization Center: two decades of high-throughput crystallization efforts fueled by structural genomics","authors":"Gabrielle R. Budziszewski, Tiffany R. Wright, M. E. Snell, Miranda L. Lynch, Sarah E J Bowman","doi":"10.1107/s205327332309928x","DOIUrl":"https://doi.org/10.1107/s205327332309928x","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323097917
Aaron T. Smith
{"title":"Challenges and successes in determining the structure of arginyltransferase 1 (ATE1)","authors":"Aaron T. Smith","doi":"10.1107/s2053273323097917","DOIUrl":"https://doi.org/10.1107/s2053273323097917","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323098054
Michael R. Rankin, D. Khare, Estefanía Martínez Valdivia, David H. Sherman, W. Gerwick, A. Mapp, Janet L. Smith
{"title":"Structural and biochemical investigation of a novel natural product amination domain","authors":"Michael R. Rankin, D. Khare, Estefanía Martínez Valdivia, David H. Sherman, W. Gerwick, A. Mapp, Janet L. Smith","doi":"10.1107/s2053273323098054","DOIUrl":"https://doi.org/10.1107/s2053273323098054","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323098960
H. Choe
Na 0.5Bi0.5TiO 3 (NBT) is interesting as a potential lead-free piezoelectric and intriguing as the model system for the crystallography of perovskites. The average / local structures of NBT are frequently debated, while their relationship to the physical properties is unclear. The previous reports [1] of the monoclinic (Cc) average symmetry of NBT structure motivate for the in-depth studies of the processes, which are triggered to the polarization rotation and its implication for the physical properties. It is therefore particularly interesting to investigate the response of NBT to such external influences as electric field, change of a temperature or high-pressure, where polarization rotation may be observed and described. The aim of this work is to probe the lattice response of NBT single crystal to an external electric field. We implemented stroboscopic time-resolved X -ray diffraction (descripted in [2]) to acquire high -resolution reciprocal space maps as a functi on of time and triangular-shaped 100 Hz cyclic electric field. We focused at the reciprocal space region around {004} reflection and carefully mapped it in -situ using state-of -the- art X - ray optics and synchrotron radiation source (P08 beamline at PETRA III and KMC-3 XPP at BESSY II). We observed that reciprocal space maps are separated into two peak components, where the separation magnitude follows electric field (see the figure). The similar radial separation of {00l} was used as the evidence of non - rhombohe dral (monoclinic) average symmetry in NBT [1]. We analysed this separation by fi tting the observed two -dimensional intensity maps with a pair of two -dimensional Pseudo-Voigt functions to track the individual peaks independently. The results are discussed in the framework of the proposed monoclinic symmetry and allowed polarization rotation.
Na 0.5Bi0.5TiO 3（NBT）作为一种潜在的无铅压电体非常有趣，而作为包晶石晶体学的模型系统也非常引人入胜。NBT 的平均/局部结构经常引起争议，而它们与物理性质的关系却不清楚。之前关于 NBT 结构的单斜（Cc）平均对称性的报道 [1] 促使人们深入研究引发极化旋转的过程及其对物理性质的影响。因此，研究 NBT 对电场、温度变化或高压等外部因素的反应尤为有趣，因为在这种情况下可以观察和描述极化旋转。这项工作的目的是探测 NBT 单晶对外部电场的晶格响应。我们采用频闪时间分辨 X 射线二折射技术（见文献 [2]）来获取高分辨率的倒易空间图，并将其作为时间和三角形 100 Hz 循环电场的函数。我们聚焦于{004}重射周围的倒易空间区域，并使用最先进的 X 射线光学仪器和同步辐射源（佩特拉三期的 P08 光束线和 BESSY 二期的 KMC-3 XPP）对其进行了仔细的原位测绘。我们观察到，倒易空间图被分成两个峰值成分，其分离程度与电场有关（见图）。{00l}的类似径向分离被用作 NBT 中非斜方晶系（单斜晶系）平均对称性的证据[1]。我们用一对二维伪伏依格特函数对观察到的二维强度图进行了分析，以独立跟踪各个峰值。我们在所提出的单斜对称性和允许偏振旋转的框架内对结果进行了讨论。
{"title":"Time-resolved reciprocal-space mapping of ferroelectric perovskites under an alternating electric field","authors":"H. Choe","doi":"10.1107/s2053273323098960","DOIUrl":"https://doi.org/10.1107/s2053273323098960","url":null,"abstract":"Na 0.5Bi0.5TiO 3 (NBT) is interesting as a potential lead-free piezoelectric and intriguing as the model system for the crystallography of perovskites. The average / local structures of NBT are frequently debated, while their relationship to the physical properties is unclear. The previous reports [1] of the monoclinic (Cc) average symmetry of NBT structure motivate for the in-depth studies of the processes, which are triggered to the polarization rotation and its implication for the physical properties. It is therefore particularly interesting to investigate the response of NBT to such external influences as electric field, change of a temperature or high-pressure, where polarization rotation may be observed and described. The aim of this work is to probe the lattice response of NBT single crystal to an external electric field. We implemented stroboscopic time-resolved X -ray diffraction (descripted in [2]) to acquire high -resolution reciprocal space maps as a functi on of time and triangular-shaped 100 Hz cyclic electric field. We focused at the reciprocal space region around {004} reflection and carefully mapped it in -situ using state-of -the- art X - ray optics and synchrotron radiation source (P08 beamline at PETRA III and KMC-3 XPP at BESSY II). We observed that reciprocal space maps are separated into two peak components, where the separation magnitude follows electric field (see the figure). The similar radial separation of {00l} was used as the evidence of non - rhombohe dral (monoclinic) average symmetry in NBT [1]. We analysed this separation by fi tting the observed two -dimensional intensity maps with a pair of two -dimensional Pseudo-Voigt functions to track the individual peaks independently. The results are discussed in the framework of the proposed monoclinic symmetry and allowed polarization rotation.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323099230
Kent Griffith
{"title":"Complex host structures and phase transitions in fast-charging lithium-ion battery anodes from diffraction and complementary techniques","authors":"Kent Griffith","doi":"10.1107/s2053273323099230","DOIUrl":"https://doi.org/10.1107/s2053273323099230","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323096730
Yimin Mao
{"title":"Hierarchical structures of polysaccharides","authors":"Yimin Mao","doi":"10.1107/s2053273323096730","DOIUrl":"https://doi.org/10.1107/s2053273323096730","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"199 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323099758
Wen Wang, Wayne A. Hendrickson
Crystals of large macromolecular complexes often diffract quite poorly, typically having high solvent content, relatively feeb le lattice contacts, quite weak subunit associations, and somewhat fl exible interdomain linkages. Although resolution may be limited to dmin > 7-8 Å, the diffraction amplitudes should suffice, in principle, to specify conformational torsion angles; however, at such ultralow resolution, realizing and maintaining a suitable model within the radius of refinement convergence is a challenge. Important insights into biological processes may be obtained, but only if structural validity can be assured. Having successfully refined a four - copy structure of Hsp70 DnaK in the S-state at 7.7 Å resolution as rigid bodies (Wang et al. , Mol. Cell 81 , 3919, 2021), we set out to refine a crystal structure of ryanodine receptor RyR1 at 8.0 Å resolution by having multiple quasi - rigid bodies to comprise the 5037 residues in each protomer of the RyR1 -tetramer as complexed with calstabin. After molecular replacement from a 65% -complete cryo-EM model at 3.6 Å resolution (des Georges et al. , Cell 167 , 145, 2016), the structure was refined from a single rigid-body (R free = 0.53), through five linked rigid bodies (R free = 0.47), and fi nally as 18 linked domains (R free = 0.43) identified in the cryo-EM analysis and then sub-divided as dictated by (F o - F c ) difference map and the R free analysis. We then turned to AlphaFold, presuming that the process had stalled due to incompleteness and uncertainty in the initial model. Trials showed that AlphaFold - predicted domains reduced Rfree when fitted into crystal density. We then systematically identified such AlphaFold - modeled domains and obtained substantial improvement (Rfree = 0.38). Further improvement followed after Rosetta refinement using tight restraints in the phenix.rosetta_refine module (R free
大分子复合物晶体的衍射效果通常很差，通常具有较高的溶剂含量、相对较弱的晶格接触、较弱的亚基关联以及一定程度的易域间连接。虽然分辨率可能被限制在 dmin > 7-8 Å，但原则上，二维衍射振幅应该可以指定构象扭转角；然而，在如此超低的分辨率下，实现并维持一个合适的模型在衍射收敛半径内是一个挑战。只有确保结构的有效性，才能获得对生物过程的重要见解。在以 7.7 Å 分辨率的刚体成功重塑了 S 状态下 Hsp70 DnaK 的四副本结构之后（Wang 等人，Mol. Cell 81 , 3919, 2021），我们开始以 8.0 Å 分辨率重塑雷诺丁受体 RyR1 的晶体结构，方法是用多个准刚体组成与 calstabin 复合物的 RyR1 四聚体每个原体中的 5037 个残基。从分辨率为 3.6 Å 的 65% 完整冷冻电镜模型（des Georges 等人，Cell 167 , 145, 2016 年）进行分子置换后，该结构从单一刚体（R free = 0.53），到五个链接刚体（R free = 0.47），最后是冷冻电镜分析中确定的 18 个链接结构域（R free = 0.43），然后根据（F o - F c ）差图和 R free 分析进行细分。然后，我们转向 AlphaFold，假定由于初始模型的不完整性和不确定性，这一过程已经停滞。试验结果表明，AlphaFold 预测的结构域与晶体密度结合后，Rfree 值降低了。随后，我们系统地识别了这些 AlphaFold 建模域，并获得了大幅改善（Rfree = 0.38）。在使用 phenix.rosetta_refine 模块中的严格约束条件对 Rosetta 进行重构后，结果得到了进一步改善（R free = 0.38）。
{"title":"Refinement of crystal structures at ultralow resolution with assistance from AlphaFold modeling and Rosetta optimization","authors":"Wen Wang, Wayne A. Hendrickson","doi":"10.1107/s2053273323099758","DOIUrl":"https://doi.org/10.1107/s2053273323099758","url":null,"abstract":"Crystals of large macromolecular complexes often diffract quite poorly, typically having high solvent content, relatively feeb le lattice contacts, quite weak subunit associations, and somewhat fl exible interdomain linkages. Although resolution may be limited to dmin > 7-8 Å, the diffraction amplitudes should suffice, in principle, to specify conformational torsion angles; however, at such ultralow resolution, realizing and maintaining a suitable model within the radius of refinement convergence is a challenge. Important insights into biological processes may be obtained, but only if structural validity can be assured. Having successfully refined a four - copy structure of Hsp70 DnaK in the S-state at 7.7 Å resolution as rigid bodies (Wang et al. , Mol. Cell 81 , 3919, 2021), we set out to refine a crystal structure of ryanodine receptor RyR1 at 8.0 Å resolution by having multiple quasi - rigid bodies to comprise the 5037 residues in each protomer of the RyR1 -tetramer as complexed with calstabin. After molecular replacement from a 65% -complete cryo-EM model at 3.6 Å resolution (des Georges et al. , Cell 167 , 145, 2016), the structure was refined from a single rigid-body (R free = 0.53), through five linked rigid bodies (R free = 0.47), and fi nally as 18 linked domains (R free = 0.43) identified in the cryo-EM analysis and then sub-divided as dictated by (F o - F c ) difference map and the R free analysis. We then turned to AlphaFold, presuming that the process had stalled due to incompleteness and uncertainty in the initial model. Trials showed that AlphaFold - predicted domains reduced Rfree when fitted into crystal density. We then systematically identified such AlphaFold - modeled domains and obtained substantial improvement (Rfree = 0.38). Further improvement followed after Rosetta refinement using tight restraints in the phenix.rosetta_refine module (R free","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"373 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：