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Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1104-14. doi: 10.1107/S1399004714001308. Epub 2014 Mar 20.

Automated identification of elemental ions in macromolecular crystal structures.

Author information

1
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
2
Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England.
3
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
4
Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
5
Los Alamos National Laboratory, Los Alamos, NM 87545-0001, USA.
6
Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA.

Abstract

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.

KEYWORDS:

PHENIX; ions; refinement

PMID:
24699654
PMCID:
PMC3975891
DOI:
10.1107/S1399004714001308
[Indexed for MEDLINE]
Free PMC Article

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