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Title: Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions. The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.
Authors:
; ; ; ; ;  [1]
  1. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (United Kingdom)
Publication Date:
OSTI Identifier:
22347706
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal Issue: Pt 1; Other Information: PMCID: PMC4304694; PMID: 25615868; PUBLISHER-ID: ba5226; OAI: oai:pubmedcentral.nih.gov:4304694; Copyright (c) Brown et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; DENSITY; ELECTRONS; INTERATOMIC DISTANCES; MICROSCOPY; MODIFICATIONS; RELIABILITY; RESOLUTION