Real-space refinement in PHENIX for cryo-EM and crystallography

Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.; Sobolev, Oleg V.; Terwilliger, Thomas C.; Urzhumtsev, Alexandre; Adams, Paul D.

doi:10.1107/S2059798318006551

Title: Real-space refinement in PHENIX for cryo-EM and crystallography

Journal Article · 30 May 2018 · Acta Crystallographica. Section D. Structural Biology

DOI: https://doi.org/10.1107/S2059798318006551 · OSTI ID:1439491

^[1];

^[2];

^[3]; Sobolev, Oleg V. ^[2];

^[4]; Urzhumtsev, Alexandre ^[5]; Adams, Paul D. ^[6]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shanghai Univ. (China)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Cambridge (United Kingdom)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium, Los Alamos, NM (United States)
Univ. de Lorraine, Vandoeuvre-les-Nancy (France); IGBMC, CNRS–INSERM–UdS, Illkirch (France)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); French Infrastructure for Integrated Structural Biology (FRISBI); Wellcome Trust; USDOE; Wellcome Trust, London (United Kingdom)

Grant/Contract Number:: AC52-06NA25396; GM063210; AC02-05CH11231; 082961/ Z/07/Z; ANR-10-INBS-05

OSTI ID:: 1439491

Alternate ID(s):: OSTI ID: 1441336; OSTI ID: 1461166; OSTI ID: 1881870

Report Number(s):: LA-UR-18-20271; ACSDAD

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Vol. 74, Issue 6; ISSN 2059-7983

Publisher:: IUCrCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 1250 works

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De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge Terashi, Genki; Kihara, Daisuke Journal of Structural Biology, Vol. 204, Issue 2 https://doi.org/10.1016/j.jsb.2018.07.013	journal	November 2018
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Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System Wilkinson, Martin; Drabavicius, Gediminas; Silanskas, Arunas Molecular Cell, Vol. 75, Issue 1 https://doi.org/10.1016/j.molcel.2019.04.020	journal	July 2019
Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly Qiao, Shuai; Langlois, Christine R.; Chrustowicz, Jakub Molecular Cell, Vol. 77, Issue 1 https://doi.org/10.1016/j.molcel.2019.10.009	journal	January 2020
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The Respiratory Syncytial Virus Polymerase: A Multitasking Machine Fearns, Rachel Trends in Microbiology, Vol. 27, Issue 12 https://doi.org/10.1016/j.tim.2019.10.001	journal	December 2019
Cryo-EM structure of a light chain-derived amyloid fibril from a patient with systemic AL amyloidosis Radamaker, Lynn; Lin, Yin-Hsi; Annamalai, Karthikeyan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09032-0	journal	March 2019
Structures of the wild-type MexAB–OprM tripartite pump reveal its complex formation and drug efflux mechanism Tsutsumi, Kenta; Yonehara, Ryo; Ishizaka-Ikeda, Etsuko Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09463-9	journal	April 2019
Structure of the substrate-engaged SecA-SecY protein translocation machine Ma, Chengying; Wu, Xiaofei; Sun, Dongjie Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10918-2	journal	June 2019
Bypassing pan-enterovirus host factor PLA2G16 Baggen, Jim; Liu, Yue; Lyoo, Heyrhyoung Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11256-z	journal	July 2019
Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism Cuervo, Ana; Fàbrega-Ferrer, Montserrat; Machón, Cristina Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11705-9	journal	August 2019
Atomic structure of the Epstein-Barr virus portal Machón, Cristina; Fàbrega-Ferrer, Montserrat; Zhou, Daming Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11706-8	journal	August 2019
Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis Schmidt, Matthias; Wiese, Sebastian; Adak, Volkan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13038-z	journal	November 2019
Multiple conformations facilitate PilT function in the type IV pilus McCallum, Matthew; Benlekbir, Samir; Nguyen, Sheryl Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13070-z	journal	November 2019
Cryo-EM structure of the human MLL1 core complex bound to the nucleosome Park, Sang Ho; Ayoub, Alex; Lee, Young-Tae Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13550-2	journal	December 2019
Cryo-EM structure of the respiratory syncytial virus RNA polymerase Cao, Dongdong; Gao, Yunrong; Roesler, Claire Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-14246-3	journal	January 2020
Robust ultraclean atomically thin membranes for atomic-resolution electron microscopy Zheng, Liming; Chen, Yanan; Li, Ning Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14359-0	journal	January 2020
Structural ensemble of a glutamate transporter homologue in lipid nanodisc environment Arkhipova, Valentina; Guskov, Albert; Slotboom, Dirk J. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14834-8	journal	February 2020
Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Gαi1 McClelland, Levi J.; Zhang, Kaiming; Mou, Tung-Chung Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14943-4	journal	February 2020
The substrate specificity switch FlhB assembles onto the export gate to regulate type three secretion Kuhlen, Lucas; Johnson, Steven; Zeitler, Andreas Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15071-9	journal	March 2020
ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria Mühleip, Alexander; Kock Flygaard, Rasmus; Ovciarikova, Jana Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20381-z	journal	January 2021
Structural basis of RNA polymerase inhibition by viral and host factors Pilotto, Simona; Fouqueau, Thomas; Lukoyanova, Natalya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-25666-5	journal	September 2021
Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer Laverty, Duncan; Desai, Rooma; Uchański, Tomasz Nature, Vol. 565, Issue 7740 https://doi.org/10.1038/s41586-018-0833-4	journal	January 2019
Structure of replicating SARS-CoV-2 polymerase Hillen, Hauke S.; Kokic, Goran; Farnung, Lucas Nature, Vol. 584, Issue 7819 https://doi.org/10.1038/s41586-020-2368-8	journal	May 2020
Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Yan, Chunli; Dodd, Thomas; He, Yuan Nature Structural & Molecular Biology, Vol. 26, Issue 6 https://doi.org/10.1038/s41594-019-0220-3	journal	May 2019
Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic Scaiola, Alain; Leibundgut, Marc; Boehringer, Daniel Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42155-4	journal	April 2019
Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery Kumari, Jyoti; Vinnakota, Rajesh; Kumar, Janesh Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46770-z	journal	July 2019
Structural basis of light-induced redox regulation in the Calvin–Benson cycle in cyanobacteria McFarlane, Ciaran R.; Shah, Nita R.; Kabasakal, Burak V. Proceedings of the National Academy of Sciences, Vol. 116, Issue 42 https://doi.org/10.1073/pnas.1906722116	journal	September 2019
Structural basis of Q-dependent antitermination Yin, Zhou; Kaelber, Jason T.; Ebright, Richard H. Proceedings of the National Academy of Sciences, Vol. 116, Issue 37 https://doi.org/10.1073/pnas.1909801116	journal	August 2019
Insight into the multifunctional RNA synthesis machine of rabies virus Fodor, Ervin Proceedings of the National Academy of Sciences, Vol. 117, Issue 8 https://doi.org/10.1073/pnas.2000120117	journal	January 2020
Structural basis for isoform-specific inhibition of human CTPS1 Lynch, Eric M.; DiMattia, Michael A.; Albanese, Steven Proceedings of the National Academy of Sciences, Vol. 118, Issue 40 https://doi.org/10.1073/pnas.2107968118	journal	September 2021
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Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin Stephan, Hirschi,; David, Kalbermatter,; Zöhre, Ucurum, ETH Zurich https://doi.org/10.3929/ethz-b-000496959	text	January 2021
Distinct and evolutionary conserved structural features of the human nuclear exosome complex Gerlach, Piotr; Schuller, Jan M.; Bonneau, Fabien eLife, Vol. 7 https://doi.org/10.7554/elife.38686	journal	July 2018
Structural principles of SNARE complex recognition by the AAA+ protein NSF White, K. Ian; Zhao, Minglei; Choi, Ucheor B. eLife, Vol. 7 https://doi.org/10.7554/elife.38888	journal	September 2018
Structures of translationally inactive mammalian ribosomes Brown, Alan; Baird, Matthew R.; Yip, Matthew CJ eLife, Vol. 7 https://doi.org/10.7554/elife.40486	journal	October 2018
Structural and functional characterization of an otopetrin family proton channel Chen, Qingfeng; Zeng, Weizhong; She, Ji eLife, Vol. 8 https://doi.org/10.7554/elife.46710	journal	April 2019
Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands Li, Jie; Shang, Guijun; Chen, Yu-Ju eLife, Vol. 8 https://doi.org/10.7554/elife.47650	journal	September 2019
The structure of the yeast Ctf3 complex Hinshaw, Stephen M.; Dates, Andrew N.; Harrison, Stephen C. eLife, Vol. 8 https://doi.org/10.7554/elife.48215	journal	June 2019
A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex Partlow, Edward A.; Baker, Richard W.; Beacham, Gwendolyn M. eLife, Vol. 8 https://doi.org/10.7554/elife.50003	journal	August 2019
Molecular structures of the human Slo1 K+ channel in complex with β4 Tao, Xiao; MacKinnon, Roderick eLife, Vol. 8 https://doi.org/10.7554/elife.51409	journal	December 2019
Cryo-EM structure of the KvAP channel reveals a non-domain-swapped voltage sensor topology Tao, Xiao; MacKinnon, Roderick eLife, Vol. 8 https://doi.org/10.7554/elife.52164	journal	November 2019
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement Patel, Avinash B.; Moore, Camille M.; Greber, Basil J. eLife, Vol. 8 https://doi.org/10.7554/elife.54449	journal	December 2019
The structures of secretory and dimeric immunoglobulin A Kumar Bharathkar, Sonya; Parker, Benjamin W.; Malyutin, Andrey G. eLife, Vol. 9 https://doi.org/10.7554/elife.56098	journal	October 2020

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