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/s2053273323097243
Lindsey R. F. Backman
{"title":"A snowball effect of opening doors and offering sustained support for early career scientists","authors":"Lindsey R. F. Backman","doi":"10.1107/s2053273323097243","DOIUrl":"https://doi.org/10.1107/s2053273323097243","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":"139361631","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/s2053273323096237
Madeline M. Glennon, Krishna M. Shivakumar, Martina Zafferani, Anita Donlic, Amanda E. Hargrove, Jessica A. Brown
Three - dimensional (3D) structures of drug targets have been essential in drug design and discovery. Cryogenic -electron microscopy (cryo-EM) is a revolutionary method that has been successful for elucidating the 3D structures of macromolecules, including small RNAs. However, only a handful of RNA - only 3D structures have been solved and none are in complex with a drug-like small molecule. Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a nuclear -retained long non-coding RNA (lncRNA) with a 3′ - terminal triple helix. The triple helix contributes to the overall stability of MALAT1 by preventing 3′ degradation, resulting in the nuclear accumulation of MALAT1. This over accumulation contributes to the onset and progression of disease, making the triple helix an alluring drug target. Small molecule therapeutics are rapidly expanding due to their deliverability, uptake, and tunability. Promising small molecule libraries comprised of the diphenylfuran (DPF) and diminazene (DMZ) scaffolds, which are known triplex-binding molecules, were developed and initially characterized for their bind ing effects on the MALAT1 triple helix by the Hargrove laboratory. Currently, there is no 3D structure of the MALAT1 triple helix in complex with a small molecule. Herein, I am working towards solving a 3D structure of the MALAT1 triple helix in complex wit h DPF/DMZ small molecules. Thus far, I have grafted the MALAT1 triple helix onto previously solved cryo - EM RNA structures to improve single particle contrast and particle picking. The apo MALAT1 triple helix has been solved at a 5.2 Å resolution; this apo structure will be a reference for density and conformational changes that occur in the presence of a small molecule. I am currently working toward a higher -resolution structure while also optimizing grid conditions for the RNA-small molecule complex. Overall, this study will provide a platform for researchers to better understand how small molecules interact with the MALAT1
{"title":"Structural characterization of a small-molecule RNA triple helix complex","authors":"Madeline M. Glennon, Krishna M. Shivakumar, Martina Zafferani, Anita Donlic, Amanda E. Hargrove, Jessica A. Brown","doi":"10.1107/s2053273323096237","DOIUrl":"https://doi.org/10.1107/s2053273323096237","url":null,"abstract":"Three - dimensional (3D) structures of drug targets have been essential in drug design and discovery. Cryogenic -electron microscopy (cryo-EM) is a revolutionary method that has been successful for elucidating the 3D structures of macromolecules, including small RNAs. However, only a handful of RNA - only 3D structures have been solved and none are in complex with a drug-like small molecule. Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a nuclear -retained long non-coding RNA (lncRNA) with a 3′ - terminal triple helix. The triple helix contributes to the overall stability of MALAT1 by preventing 3′ degradation, resulting in the nuclear accumulation of MALAT1. This over accumulation contributes to the onset and progression of disease, making the triple helix an alluring drug target. Small molecule therapeutics are rapidly expanding due to their deliverability, uptake, and tunability. Promising small molecule libraries comprised of the diphenylfuran (DPF) and diminazene (DMZ) scaffolds, which are known triplex-binding molecules, were developed and initially characterized for their bind ing effects on the MALAT1 triple helix by the Hargrove laboratory. Currently, there is no 3D structure of the MALAT1 triple helix in complex with a small molecule. Herein, I am working towards solving a 3D structure of the MALAT1 triple helix in complex wit h DPF/DMZ small molecules. Thus far, I have grafted the MALAT1 triple helix onto previously solved cryo - EM RNA structures to improve single particle contrast and particle picking. The apo MALAT1 triple helix has been solved at a 5.2 Å resolution; this apo structure will be a reference for density and conformational changes that occur in the presence of a small molecule. I am currently working toward a higher -resolution structure while also optimizing grid conditions for the RNA-small molecule complex. Overall, this study will provide a platform for researchers to better understand how small molecules interact with the MALAT1","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361636","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/s2053273323098674
Simon Fromm, Kate M. O’Connor, Michael Purdy, P. R. Bhatt, Gary Longharn, John F. Atkins, Ahmad Jomaa, Simone Mattei
{"title":"The structure of the translating bacterial ribosome at 1.55 Å resolution","authors":"Simon Fromm, Kate M. O’Connor, Michael Purdy, P. R. Bhatt, Gary Longharn, John F. Atkins, Ahmad Jomaa, Simone Mattei","doi":"10.1107/s2053273323098674","DOIUrl":"https://doi.org/10.1107/s2053273323098674","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361644","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/s2053273323099175
J. Merkelbach, Christian Jandl, Danny Stam, Sebastian Schegk
{"title":"A perfect liaison: combining MicroED with PXRD","authors":"J. Merkelbach, Christian Jandl, Danny Stam, Sebastian Schegk","doi":"10.1107/s2053273323099175","DOIUrl":"https://doi.org/10.1107/s2053273323099175","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361725","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/s2053273323097607
M. Mazzorana, David Aragao, Neil Paterson, Elliot Nelson, Felicity Bertram, Dave Hall
The MX group at Diamond Light Source offers a suite of seven macromolecular crystallography (MX) beamlines covering a variety of setups and techniques to meet the demands of the user community. This selection of instruments allows access to a wide range of focusing, energy, throughput capabilities as well as numerous approaches including in-situ , serial crystallography, and fragment - based drug discovery.
{"title":"Improving access and throughput of the MX beamlines at Diamond Light Source, UK","authors":"M. Mazzorana, David Aragao, Neil Paterson, Elliot Nelson, Felicity Bertram, Dave Hall","doi":"10.1107/s2053273323097607","DOIUrl":"https://doi.org/10.1107/s2053273323097607","url":null,"abstract":"The MX group at Diamond Light Source offers a suite of seven macromolecular crystallography (MX) beamlines covering a variety of setups and techniques to meet the demands of the user community. This selection of instruments allows access to a wide range of focusing, energy, throughput capabilities as well as numerous approaches including in-situ , serial crystallography, and fragment - based drug discovery.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361852","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/s2053273323098777
Jaime C. Van Loon, F. Le Mauff, E. Kitova, Stephanie Gilbert, Mario A. Vargas, Erum Razvi, John S. Klassen, Donald C. Sheppard, P. L. Howell
{"title":"Understanding how the Pel polysaccharide is modified for use in the Pseudomonas aeruginosa biofilm","authors":"Jaime C. Van Loon, F. Le Mauff, E. Kitova, Stephanie Gilbert, Mario A. Vargas, Erum Razvi, John S. Klassen, Donald C. Sheppard, P. L. Howell","doi":"10.1107/s2053273323098777","DOIUrl":"https://doi.org/10.1107/s2053273323098777","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362089","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/s2053273323099345
M. Woińska, S. Pawlędzio, A. Hoser, M. Chodkiewicz, K. Woźniak
Transition metal (TM) hydrides are versatile compounds with multiple applications in catalysis, energy conversion, and the search for hydrogen storage materials or superconductors. Therefore, determining the structure of these compounds with X -ray diffraction is essential for many areas of research. However, this is hampered by the challenges of locating the position of hydrogen with X - rays, which are even more aggravated in the case of hydrogen atoms bonded to a TM atom. Furthermore, collecting high - quality, let alone high-resolution X -ray d ata, for TM hydrides, is an arduous task. It is also difficult to collect neutron data that could provide reliable information about hydrogen positions. TM hydride complexes are also computationally demanding, which makes them difficult to analyze using quantu m crystallographic methods. Hirshfeld atom refinement (HAR) is a quantum crystallographic method that has been proven to locate hydrogen atoms bonded to light elements with accuracy and precision very close to that of neutron experiments, based on standard resolution X - ray data [1]. In some cases, HAR has been reported to improve the positions of hydrogen atoms in TM - H bonds considerably [1, 2], as compared to the Independent Atom Model (IAM). The goal of this study was to evaluate the capabilities of HAR in terms of establishing the positions of hydrogen atoms, especially in TM - H bonds, and to investigate the influence of different parameters adjustable in the refinement on the final result. The following factors were considered: including interactions with the crystal environment, taking into account relativistic effects, changing the DFT functional used for wave function calculations (B3LYP, PBE, M06 - 2X), and selecting the basis set. Another aspect considered in the study was the role of treatment of hydrogen thermal
过渡金属（TM）氢化物是一种用途广泛的化合物，在催化、能源转换、寻找储氢材料或超导体等方面有多种应用。因此，利用 X 射线衍射确定这些化合物的结构对许多研究领域都至关重要。然而，用 X 射线定位氢的位置是一个难题，而在氢原子与 TM 原子成键的情况下，这一难题就更加严峻。此外，收集 TM 氢化物的高质量、更不用说高分辨率 X 射线数据是一项艰巨的任务。收集可提供有关氢位置的可靠信息的中子数据也很困难。TM 氢化物复合物的计算要求也很高，这使得它们很难使用量子晶体学方法进行分析。Hirshfeld atom re-rennement（HAR）是一种量子晶体学方法，已被证明可以根据标准分辨率的 X 射线数据找到与轻元素结合的氢原子，其准确度和精确度非常接近中子实验[1]。据报道，在某些情况下，与独立原子模型（IAM）相比，HAR 能显著改善 TM - H 键中氢原子的位置[1, 2]。本研究的目的是评估 HAR 在确定氢原子位置（尤其是 TM - H 键中）方面的能力，并研究重构过程中可调整的不同参数对最终结果的影响。研究考虑了以下因素：包括与晶体环境的相互作用、相对论效应、改变波函数计算所使用的 DFT 函数（B3LYP、PBE、M06 - 2X）以及选择基集。研究考虑的另一个方面是氢热处理的作用。
{"title":"Challenges and capabilities of quantum crystallography for locating hydrogen atoms in transition metal hydrides","authors":"M. Woińska, S. Pawlędzio, A. Hoser, M. Chodkiewicz, K. Woźniak","doi":"10.1107/s2053273323099345","DOIUrl":"https://doi.org/10.1107/s2053273323099345","url":null,"abstract":"Transition metal (TM) hydrides are versatile compounds with multiple applications in catalysis, energy conversion, and the search for hydrogen storage materials or superconductors. Therefore, determining the structure of these compounds with X -ray diffraction is essential for many areas of research. However, this is hampered by the challenges of locating the position of hydrogen with X - rays, which are even more aggravated in the case of hydrogen atoms bonded to a TM atom. Furthermore, collecting high - quality, let alone high-resolution X -ray d ata, for TM hydrides, is an arduous task. It is also difficult to collect neutron data that could provide reliable information about hydrogen positions. TM hydride complexes are also computationally demanding, which makes them difficult to analyze using quantu m crystallographic methods. Hirshfeld atom refinement (HAR) is a quantum crystallographic method that has been proven to locate hydrogen atoms bonded to light elements with accuracy and precision very close to that of neutron experiments, based on standard resolution X - ray data [1]. In some cases, HAR has been reported to improve the positions of hydrogen atoms in TM - H bonds considerably [1, 2], as compared to the Independent Atom Model (IAM). The goal of this study was to evaluate the capabilities of HAR in terms of establishing the positions of hydrogen atoms, especially in TM - H bonds, and to investigate the influence of different parameters adjustable in the refinement on the final result. The following factors were considered: including interactions with the crystal environment, taking into account relativistic effects, changing the DFT functional used for wave function calculations (B3LYP, PBE, M06 - 2X), and selecting the basis set. Another aspect considered in the study was the role of treatment of hydrogen thermal","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362166","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/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}
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