Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skewness of electron density with the local correlation of r.m.s. density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol wizard carries out automated structure solution based on any combination of SAD, MAD, SIR or MIR data sets. The wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing.
Terwilliger
Thomas C
TC
Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov
Adams
Paul D
PD
Read
Randy J
RJ
McCoy
Airlie J
AJ
Moriarty
Nigel W
NW
Grosse-Kunstleve
Ralf W
RW
Afonine
Pavel V
PV
Zwart
Peter H
PH
Hung
Li Wei
LW
D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D003460:Crystallization; D018360:Crystallography, X-Ray; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D046912:Multiprotein Complexes / Q000737:chemistry*; D011487:Protein Conformation; D015203:Reproducibility of Results; D012107:Research Design; D012984:Software
D046912:Multiprotein Complexes