Automated identification of elemental ions in macromolecular crystal structures.
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.
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
Nathaniel
N
Echols
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
Nader
N
Morshed
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
Pavel V
PV
Afonine
Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England.
Airlie J
AJ
McCoy
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Mitchell D
MD
Miller
Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England.
Randy J
RJ
Read
Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
Jane S
JS
Richardson
Los Alamos National Laboratory, Los Alamos, NM 87545-0001, USA.
Thomas C
TC
Terwilliger
Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA.
Paul D
PD
Adams
D057205:Automation, Laboratory / Q000379:methods*; D018360:Crystallography, X-Ray / Q000379:methods*; D007477:Ions / Q000737:chemistry; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D013820:Thermolysin / Q000737:chemistry; D013917:Thrombin / Q000737:chemistry
D007477:Ions; D013917:Thrombin; D013820:Thermolysin
PHENIX; ions; refinement