Table 1. R factors, Ramachandran plot outliers (RO) and MolProbity clashscores (CS; Davis et al., 2007 ▶) for selected structures extracted from the PDB (published), extracted from PDB_REDO and after refinement using phenix.refine .
All data cutoffs (resolution, ) were applied as reported in the original works in order to maintain the same reflections used in the calculations.
| Extracted from REMARK records of PDB file header | Calculated with PHENIX from original PDB† | PDB_REDO ‡ | Re-refined in phenix.refine § | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Code¶ | d min () | Data source | R work/R free (%) | R work/R free (%) | RO (%) | CS | R work/R free (%) | RO (%) | CS | R work/R free (%) | RO (%) | CS |
| 1jl4 | 4.3 | X-ray | 42.0/45.3 | 34.2/37.0 | 0.74 | 40.0 | 23.9/31.4 | 0.74 | 25.8 | 24.2/30.9 | 0.92 | 13.3 |
| 2gsz | 4.2 | X-ray | 34.3/40.6 | 31.0/36.1 | 1.33 | 37.1 | 34.3/39.9 | 1.33 | 37.1 | 25.8/32.7 | 0.98 | 25.7 |
| 1yi5 | 4.2 | X-ray | 33.1/37.8 | 30.3/33.9 | 2.79 | 17.6 | 24.1/31.1 | 2.86 | 15.9 | 25.9/28.5 | 0.98 | 15.5 |
| 2wjx | 4.1 | X-ray | 29.0/35.4 | 33.7/37.0 | 0.28 | 24.5 | 33.8/36.7 | 0.28 | 24.6 | 28.5/31.9 | 0.28 | 11.8 |
| 1av1 | 4.0 | X-ray | 38.2/42.8 | 35.1/38.4 | 1.26 | 55.4 | 35.1/40.1 | 1.01 | 58.1 | 33.3/36.3 | 0.50 | 16.1 |
| 3bbw | 4.0 | X-ray | 30.2/35.4 | 21.8/22.8 | 2.82 | 21.6 | 18.4/19.9 | 1.32 | 15.9 | 18.1/21.5 | 0.94 | 11.1 |
| 2i07 | 4.0 | X-ray | 27.3/32.3 | 26.8/28.7 | 2.04 | 24.9 | 22.5/28.5 | 1.84 | 20.4 | 21.5/26.4 | 0.79 | 14.6 |
| 3eob | 3.6 | X-ray | 26.7/33.3 | 26.7/33.5 | 2.08 | 40.4 | 27.6/34.5 | 2.08 | 40.5 | 26.8/29.3 | 0.50 | 12.6 |
| 1dqv | 3.2 | X-ray | 29.3/34.8 | 30.2/na†† | 10.3 | 93.1 | na | na | na | 22.2/25.5 | 0.37 | 24.8 |
| 1c57 | 2.4 | Neutron | 27.0/30.1 | 30.0/33.9 | 0 | 6.2 | na | na | na | 20.4/25.7 | 0 | 11.2 |
| 1jmc | 2.4 | X-ray | 21.2/33.0 | 20.1/31.6 | 1.69 | 31.0 | 21.5/28.9 | 1.69 | 14.6 | 22.0/27.2 | 1.27 | 16.4 |
| 1eic | 1.4 | X-ray | 20.1/25.4 | 20.1/25.2 | 0.82 | 21.7 | 16.0/17.7 | 0.82 | 11.9 | 12.9/15.9 | 0.82 | 20.0 |
| 2elg | 1.0 | X-ray | 23.2/24.7 | 22.85/na | 0 | 7.3 | 14.1/16.9 | 0 | 2.4 | 14.1/16.0 | 0 | 7.3 |
| 1g2y | 1.0 | X-ray | 19.5/19.8 | 19.7/19.0 | 0.89 | 10.0 | 16.1/17.5 | 0.89 | 8.6 | 14.4/15.3 | 0.89 | 15.5 |
| 2ppn | 0.92 | X-ray | 20.9/19.9 | 20.4/19.8 | 0 | 8.1 | 15.4/16.0 | 0 | 8.6 | 13.3/14.7 | 0 | 14.6 |
| ur0013 | 0.65 | Neutron | 9.5/na | 9.1/na | 0 | 0 | na | na | na | 7.8/9.6 | 0 | 0 |
Calculated in PHENIX after applying resolution and cutoffs, as reported in the PDB file header.
R factors as reported on the PDB_REDO web site (Joosten et al., 2009 ▶; http://www.cmbi.ru.nl/pdb_redo/); RO and CS computed using PHENIX.
Re-refinement of PDB-deposited structures using phenix.refine. Refinement strategy (model parameterization and number of refinement macro-cycles) varies depending on model and data quality. See text for details.
PDB or NDB (Berman et al., 1992 ▶) code.
na, value is not available either owing to a missing cross-validation set of reflections or the entry is not available in the database.