Table 1. Data-collection and refinement statistics for S. agalactiae GAPDH (PDB entry 4qx6).
Values in parentheses are for the highest resolution shell.
| Wavelength () | 0.97918 |
| Space group | P21 |
| Unit-cell parameters (, ) | a = 67.77, b = 107.86, c = 90.93, = = 90, = 106.57 |
| Data-collection statistics | |
| Resolution limits () | 107.862.46 (2.592.46) |
| R merge † | 0.091 (1.015) |
| R meas † | 0.107 (1.181) |
| R p.i.m. † | 0.055 (0.601) |
| Total No. of observations | 170091 (24948) |
| No. of reflections | 45263 (6546) |
| Mean I/(I) | 13.8 (1.3) |
| CC1/2 | 0.996 (0.567) |
| Completeness (%) | 99.3 (99.0) |
| Multiplicity | 3.8 (3.8) |
| Refinement statistics | |
| Resolution range () | 64.962.46 (2.522.46) |
| No. of unique reflections | 45232 (3296) |
| R cryst ‡ (%) | 20.4 (34.5) |
| R free ‡ (%) | 23.8 (35.2) |
| No. of protein residues | 1345 |
| No. of NAD molecules | 4 |
| No. of EDO molecules | 2 |
| No. of water molecules | 126 |
| Wilson B factor (2) | 48.4 |
| Average B factors (2) | |
| Overall | 57.4 |
| Protein | 57.8 |
| NAD | 46.0 |
| EDO | 62.0 |
| Water | 42.1 |
| Coordinate error (maximum likelihood) | 0.26 |
| Correlation coefficient, F o F c | 0.95 |
| Correlation coefficient, F o F c free | 0.93 |
| Overall map CC (F c, 2mF o DF c) | 0.76§ |
| Ramachandran allowed (%) | 99.8 |
| Ramachandran disallowed (%) | 0.2 |
| MolProbity clash score | 3.4 [100th percentile] |
| MolProbity score | 1.5 [99th percentile] |
†
R meas and R p.i.m. were calculated with SCALA (Evans, 2006 ▶) in the CCP4 program suite (Winn et al., 2011 ▶) using unmerged and unscaled data preprocessed by XDS (Kabsch, 2010a ▶,b ▶). R meas is a merging R factor independent of data redundancy, while R p.i.m. provides the precision of the averaged measurement, which improves with higher multiplicity (Weiss, 2001 ▶).
‡
The data included in the R free set (5%) were excluded from refinement.
§
The value based on map calculation in PHENIX (Adams et al., 2010 ▶).