phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Abstract

phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed.

Figure 1

Example phenix.model_vs_data output (for PDB entry 3dcv). Model information includes composition and geometry statistics. Data information includes completeness in resolution shells. Model-to-data fit information includes R factors calculated for the whole set of structure factors using an optimized bulk-solvent model, anisotropic scaling, and TLS and twinning if applicable. R factors are also recalculated after applying the resolution limits and σ cutoffs reported in the PDB header.

Figure 2

Histogram of differences between R _work reported in the PDB file header and the value calculated with phenix.model_vs_data. Resolution and σ cutoffs were applied in the calculation if available.

Figure 3

Differences between R _work computed for the original structures with H atoms and the same structures after removal of the H atoms, shown as function of resolution. See §3.1.5 for details.

Figure 4

Differences between R _work values (shown as function of resolution) computed for structures without H atoms and the same structures with restored H atoms based on ideal geometry. The atomic displacement parameter and occupancy of each restored H atom was set to be identical to those of the bonded atom. See §3.1.5 for details.