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

  • PMC3975891

Electronic International Standard Serial Number (EISSN)

  • 1399-0047

Digital Object Identifier (DOI)

  • 10.1107/S1399004714001308


  • eng

Conference Location

  • United States