Title: 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:

Afonine, Pavel V.  ^[1];

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Poon, Billy K.  ^[2];

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Read, Randy J.  ^[3];

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Sobolev, Oleg V. ^[2]; Terwilliger, Thomas C.  ^[4];

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

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+ Show Author Affiliations

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:

2018-06-01

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