Automated identification of elemental ions in macromolecular crystal structures.
Journal Article (Journal Article)
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.
Full Text
Duke Authors
Cited Authors
- Echols, N; Morshed, N; Afonine, PV; McCoy, AJ; Miller, MD; Read, RJ; Richardson, JS; Terwilliger, TC; Adams, PD
Published Date
- April 2014
Published In
Volume / Issue
- 70 / Pt 4
Start / End Page
- 1104 - 1114
PubMed ID
- 24699654
Pubmed Central ID
- 24699654
Electronic International Standard Serial Number (EISSN)
- 1399-0047
Digital Object Identifier (DOI)
- 10.1107/S1399004714001308
Language
- eng
Conference Location
- United States