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Title: Automated identification of elemental ions in macromolecular crystal structures

The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.
Authors:
; ;  [1] ;  [2] ;  [3] ;  [4] ;  [2] ;  [5] ;  [6] ;  [7] ;  [4]
  1. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States)
  2. University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY (United Kingdom)
  3. SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States)
  4. (United States)
  5. Duke University Medical Center, Durham, NC 27710 (United States)
  6. Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States)
  7. University of California at Berkeley, Berkeley, CA 94720-1762 (United States)
Publication Date:
OSTI Identifier:
22347791
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 70; Journal Issue: Pt 4; Other Information: PMCID: PMC3975891; PMID: 24699654; PUBLISHER-ID: lv5059; OAI: oai:pubmedcentral.nih.gov:3975891; Copyright (c) Echols et al. 2014; 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; ALGORITHMS; ATOMS; CALCIUM; CRYSTAL STRUCTURE; CRYSTALS; DENSITY; ELECTRON DENSITY; ELECTRONS; IONS; IRON; MOLECULES; SCATTERING; SODIUM; ZINC