Real-space refinement in PHENIX for cryo-EM and crystallography
Abstract
This article describes the implementation of real-space refinement in thephenix.real_space_refineprogram from thePHENIXsuite. 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_refinemakes 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.
- Authors:
-
[1];
[2];
[3];
[4];
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Shanghai Univ. (China). Dept. of Physics and International Centre for Quantum and Molecular Structures
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
- Univ. of Cambridge (United Kingdom). Cambridge Inst. for Medical Research
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium (NMC), Los Alamos, NM (United States)
- Univ. of Lorraine, Vandoeuvre-les-Nancy (France). Faculty of Science and Technology; Inst. of Genetics and Molecular and Cell Biology (IGBMC), CNRS-INSERM-UdS, Illkirch (France). Centre for Integrative Biology
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- National Institutes of Health (NIH); French Infrastructure for Integrated Structural Biology (FRISBI); Wellcome Trust, London (United Kingdom); USDOE Office of Science (SC)
- OSTI Identifier:
- 1439491
- Alternate Identifier(s):
- OSTI ID: 1441336; OSTI ID: 1461166
- Report Number(s):
- LA-UR-18-20271
Journal ID: ISSN 2059-7983; ACSDAD; PII: S2059798318006551
- Grant/Contract Number:
- AC52-06NA25396; GM063210; AC02-05CH11231; 082961/ Z/07/Z; ANR-10-INBS-05
- Resource Type:
- Published Article
- Journal Name:
- Acta Crystallographica. Section D. Structural Biology
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Volume: 74 Journal Issue: 6; Journal ID: ISSN 2059-7983
- Publisher:
- IUCr
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; Biological Science
Citation Formats
Afonine, Pavel V., Poon, Billy K., Read, Randy J., Sobolev, Oleg V., Terwilliger, Thomas C., Urzhumtsev, Alexandre, and Adams, Paul D. Real-space refinement in PHENIX for cryo-EM and crystallography. United Kingdom: N. p., 2018.
Web. https://doi.org/10.1107/S2059798318006551.
Afonine, Pavel V., Poon, Billy K., Read, Randy J., Sobolev, Oleg V., Terwilliger, Thomas C., Urzhumtsev, Alexandre, & Adams, Paul D. Real-space refinement in PHENIX for cryo-EM and crystallography. United Kingdom. https://doi.org/10.1107/S2059798318006551
Afonine, Pavel V., Poon, Billy K., Read, Randy J., Sobolev, Oleg V., Terwilliger, Thomas C., Urzhumtsev, Alexandre, and Adams, Paul D. Fri .
"Real-space refinement in PHENIX for cryo-EM and crystallography". United Kingdom. https://doi.org/10.1107/S2059798318006551.
@article{osti_1439491,
title = {Real-space refinement in PHENIX for cryo-EM and crystallography},
author = {Afonine, Pavel V. and Poon, Billy K. and Read, Randy J. and Sobolev, Oleg V. and Terwilliger, Thomas C. and Urzhumtsev, Alexandre and Adams, Paul D.},
abstractNote = {This article describes the implementation of real-space refinement in thephenix.real_space_refineprogram from thePHENIXsuite. 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_refinemakes 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.},
doi = {10.1107/S2059798318006551},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 6,
volume = 74,
place = {United Kingdom},
year = {2018},
month = {6}
}
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