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

This work 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.
Authors:
ORCiD logo [1] ; ORCiD logo [2] ; ORCiD logo [3] ;  [2] ; ORCiD logo [4] ;  [5] ;  [6]
  1. 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
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
  3. Univ. of Cambridge (United Kingdom). Cambridge Inst. for Medical Research
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium (NMC), Los Alamos, NM (United States)
  5. 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
  6. 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:
Report Number(s):
LA-UR-18-20271
Journal ID: ISSN 2059-7983; ACSDAD
Grant/Contract Number:
AC52-06NA25396; GM063210; AC02-05CH11231; 082961/ Z/07/Z; ANR-10-INBS-05
Type:
Published Article
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 74; Journal Issue: 6; Journal ID: ISSN 2059-7983
Publisher:
IUCr
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)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; real-space refinement; cryo-EM; crystallography; map interpolation; atomic-centered targets; PHENIX
OSTI Identifier:
1439491
Alternate Identifier(s):
OSTI ID: 1441336; OSTI ID: 1461166