Automated identification of elemental ions in macromolecular crystal structures
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235 (United States)
- University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY (United Kingdom)
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States)
- Duke University Medical Center, Durham, NC 27710 (United States)
- Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States)
- University of California at Berkeley, Berkeley, CA 94720-1762 (United States)
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.
- OSTI ID:
- 22347791
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 70, 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); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
Similar Records
Using support vector machines to improve elemental ion identification in macromolecular crystal structures
Automated Structure Solution with the PHENIX Suite