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

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          Abstract

          A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.

          Abstract

          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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          Author and article information

          Conference
          Acta Crystallogr D Struct Biol
          Acta Crystallogr D Struct Biol
          Acta Cryst. D
          Acta Crystallographica. Section D, Structural Biology
          International Union of Crystallography
          2059-7983
          01 June 2018
          30 May 2018
          30 May 2018
          : 74
          : Pt 6 ( publisher-idID: d180600 )
          : 531-544
          Affiliations
          [a ]Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
          [b ]Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University , Shanghai 200444, People’s Republic of China
          [c ]Cambridge Institute for Medical Research, University of Cambridge , Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
          [d ]Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA
          [e ] New Mexico Consortium , Los Alamos, NM 87545, USA
          [f ]Faculté des Sciences et Technologies, Université de Lorraine , BP 239, 54506 Vandoeuvre-les-Nancy, France
          [g ]Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS , 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
          [h ]Department of Bioengineering, University of California Berkeley , Berkeley, California, USA
          Author notes
          Correspondence e-mail: pafonine@ 123456lbl.gov
          Article
          ic5103 ACSDAD S2059798318006551
          10.1107/S2059798318006551
          6096492
          29872004
          291a9699-41fe-4b4f-94fd-a623df6d7f19
          © Afonine et al. 2018

          This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

          Proceedings of the third CCP-EM Spring Symposium
          Page count
          Pages: 14
          Funding
          Funded by: National Institutes of Health
          Award ID: GM063210
          Funded by: PHENIX Industrial Consortium
          Funded by: U.S. Department of Energy
          Award ID: DE-AC02-05CH11231
          Funded by: French Infrastructure for Integrated Structural Biology
          Award ID: ANR-10-INBS-05
          Funded by: Wellcome Trust
          Award ID: 082961/ Z/07/Z
          Award Recipient : Randy J. Read
          This work was funded by National Institutes of Health grant GM063210. PHENIX Industrial Consortium grant . U.S. Department of Energy grant DE-AC02-05CH11231. French Infrastructure for Integrated Structural Biology grant ANR-10-INBS-05. Wellcome Trust grant 082961/ Z/07/Z to Randy J. Read.
          Categories
          Research Papers

          real-space refinement,cryo-em,crystallography,map interpolation,atomic-centered targets,phenix

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