Table 4.
Structure refinement statistics
| Crystals (PDB ID codes) | IO10 (7D5X) | IO20 (7D5W) | IO80 (7CP5) | Fully reduced forma (5B1B) |
|---|---|---|---|---|
| Resolution (Å) | 39.70–1.74 (1.76–1.74) | 39.92–1.84 (1.86–1.84) | 39.91–1.76 (1.78–1.76) | 39.90–1.60 (1.62–1.60) |
| Number of reflections in work set | 629,954 (20,340) | 533,026 (17,436) | 609,364 (20,207) | 794,473 (26,295) |
| Number of reflections in test set | 33,287 (1074) | 28,279 (893) | 32,218 (1043) | 41,978 (1408) |
| Rwork (%) | 15.59 (23.56) | 15.31 (21.47) | 16.03 (25.78) | 16.84 (23.68) |
| Rfree (%) | 18.36 (26.28) | 18.41 (24.74) | 18.86 (28.79) | 19.10 (27.18) |
| Non-hydrogen atom numbers | ||||
| Total | 33,923 | 34,545 | 34,258 | 34,425 |
| Proteins | 29,171 | 29,284 | 29,381 | 29,067 |
| Lipids | 1297 | 1287 | 1133 | 1264 |
| Detergents | 509 | 639 | 482 | 531 |
| Water | 2612 | 2975 | 2968 | 3305 |
| Ethylene glycol | 324 | 320 | 284 | 248 |
| Phosphate | 10 | 10 | 10 | 10 |
| Ligands | 4 | 8 | 8 | 0 |
| R.m.s. deviations | ||||
| Bonds (Å) | 0.020 | 0.018 | 0.017 | 0.019 |
| Angles (°) | 1.85 | 1.64 | 1.59 | 1.63 |
| Ramachandran statistics | ||||
| Favoured (%) | 96.71 | 96.88 | 96.99 | 96.97 |
| Allowed (%) | 2.98 | 2.63 | 2.58 | 2.80 |
| Outliers (%) | 0.32 | 0.49 | 0.43 | 0.23 |
| Clashscore | 6.69 | 6.65 | 5.43 | 4.65 |
| Average B-factor (Å2) | ||||
| Overall | 40.5 | 41.1 | 40.3 | 38.5 |
| Protein (Ab) | 35.7 | 35.1 | 34.7 | 32.2 |
| Protein (Bb) | 40.4 | 40.4 | 40.7 | 38.1 |
| Others | 55.7 | 59.3 | 55.5 | 56.5 |
a
The atomic parameters were revised by the present work.
b
A and B indicate monomers A and B, respectively.