TABLE 2.
Refinement statistics
| Parameter | Value for data set |
||
|---|---|---|---|
| Native, with HgCl2 | cRbdA-GTP/Mg2+ | cRbdA–c-di-GMP | |
| Data range (Å) | 70.20–2.28 (2.35–2.28) | 27.55–2.80 (2.97–2.80) | 48.70–3.31 (3.63–3.31) |
| No. of reflections used for refinement | 33,717 (2,884) | 18,292 (2,774) | 11,285 (2,663) |
| No. of nonhydrogen protein atoms | 4,318 | 4,294 | 4,295 |
| Rworka (%) | 0.193 (0.224) | 0.172 (0.195) | 0.174 (0.167) |
| Rfreeb (%) | 0.229 (0.276) | 0.255 (0.259) | 0.259 (0.272) |
| CC Fo-Fc | 0.938 | 0.927 | 0.922 |
| RMSD | |||
| Bond length (Å) | 0.010 | 0.010 | 0.010 |
| Bond angle (°) | 1.11 | 1.19 | 1.21 |
| BWilson/Boverall (Å2) | 44.3/52.0 | 55.4/44.7 | 93.4/57.0 |
| Estimated coordinate error (Å)c | 0.19 | 0.36 | 0.53 |
| Mean B factor (Å2) | |||
| Protein | 38.8 | 45.0 | 58.1 |
| Ligands | |||
| c-di-GMP | 78.5 (46) | ||
| GTP | 47.2 (32) | ||
| Mg2+ | 18.9 (1) | ||
| Water molecules (no.) | 38.9 (303) | 40.0 (315) | 37.4 (162) |
| No. (%) of residues in Ramachandran plot | |||
| Most favored | 531 (97.1) | 518 (95.2) | 509 (93.6) |
| Allowed | 15 (2.7) | 22 (4.1) | 33 (6.1) |
| Disallowed | 1 (0.2) | 4 (0.7) | 2 (0.4) |
| PDB code | 5XGB | 5XGD | 5XGE |
a
Rwork = ∑||Fo| − |Fc||/∑|Fc|, where Fo denotes the observed structure factor amplitude and Fc denotes the structure factor amplitude calculated from the model.
b
Rfree was calculated in the same way as Rwork, but with 5% of randomly chosen reflections omitted from the refinement.
c
Estimated coordinate error is based on (dispersion precision indicator [DPI]) Rfree.