Table 1. DraNramp data collection and refinement statistics.
| Inward-open apo (Patch mutant + Fab) |
Inward-occluded apo (G45R) |
Outward-open Mn2+-bound (G223W ∆N34) |
Outward-open apo (G223W ∆N34) |
|
|---|---|---|---|---|
| PDB ID | 6D9W | 6C3I | 6BU5 | 6D91 |
| SBGrid Data Bank ID | 332, 333, 334 | 567 | 564 | 576 |
| Data Collection | ||||
| Wavelength (Å) | 1.139 | 0.9793 | 0.9792 | 0.9792 |
| Resolution range (Å) | 46.47–3.94 (4.08–3.94) | 50.00–3.00 (3.05–3.00) | 39.19–2.40 (2.49–2.40) | 38.14–2.36 (2.44–2.36) |
| Space group | I222 | P212121 | C121 | C121 |
| Unit cell (a, b, c) | 113.13, 132.08, 221.0 | 70.73, 97.85, 118.26 | 105.76, 80.39, 51.75 | 101.92, 75.51, 53.15 |
| Unit cell (α, β, γ) | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 | 90.0, 94.72, 90.0 | 90.0, 98.07, 90.0 |
| Number of crystals | 3 | 2 | ~15 | ~20 |
| Total reflections | 245867 | 66707 | 49321 | 48659 (367) |
| Unique reflections | 11791 (462) | 17206 (842) | 13983 (623) | 10998 (256) |
| Redundancy | 16.6 (11.4) | 3.9 (4.0) | 3.5 (1.7) | 4.4 (1.4) |
| Completeness (%) | 95 (96) | 98.5 (98.8) | 82.1* (36.4) | 64.0* (15.6) |
| Mean I/σ(I) | 6 (.61) | 6.41 (0.95) | 6.25 (1.56) | 8.83 (1.45) |
| Rmerge | 0.171 | 0.223 (1.388) | 0.186 | 0.185 |
| Rmeas | 0.177 | 0.270 (1.608) | 0.210 | 0.203 |
| Rpim | 0.047 | 0.133 (0.795) | 0.095 | 0.080 |
| CC1/2 | 0.99 (0.189) | 0.993 (0.396) | 0.984 (0.584) | 0.986 (0.683) |
| Refinement | ||||
| Resolution range (Å) | 46.47–3.94 (4.12–3.94) | 30.0–3.0 (3.05–3.00) | 39.19–2.40 (2.49–2.40) | 39.19–2.36 (2.44–2.36) |
| Rwork | 0.271 (0.253) | 0.244 (0.328) | 0.237 (0.269) | 0.244 (0.307) |
| Rfree | 0.309 (0.343) | 0.270 (0.394) | 0.276 (0.358) | 0.299 (0.437) |
| Number of atoms | 5764 | 5979 | 3219 | 3115 |
| Protein | 5761 | 5812 | 3012 | 3012 |
| Ligand | 3 | 138 | 143 | 86 |
| Water | -- | 29 | 64 | 17 |
| Protein residues | 786 | 774 | 398 | 398 |
| Ramachandran plot | ||||
| Favored (%) | 754 (96.0) | 762 (98.4) | 389 (97.7) | 381 (95.7) |
| Allowed (%) | 32 (4.0) | 12 (1.6) | 9 (2.3) | 17 (4.3) |
| Outliers (%) | 0 (0.0) | 0 (0.0) | 0 (0.0) | 0 (0.0) |
| RMS(bonds) | 0.004 | 0.002 | 0.002 | 0.002 |
| RMS(angles) | 1.02 | 0.50 | 0.43 | 0.57 |
| Average B-factor | 90.3 | 61.27 | 73.6 | 50.1 |
| Protein | 90.3 | 61.29 | 73.1 | 49.9 |
| Ligand | 197.0 | 66.16 | 89.3 | 50.7 |
| Water | -- | 34.08 | 63.7 | 78.8 |
| Number of TLS groups | 15 | 20 | 6 | 7 |
*The G223WdN34 dataset compiled from many small crystals is 99% complete to 3.4 Å, 95% complete to 3.0 Å, 90% complete to 2.85 Å, 80% complete to 2.7 Å, and 60% complete to 2.5 Å. The G223W ΔN34 apo dataset compiled from many small crystals is 96% complete to 4.5 Å, 92% complete to 3.4 Å, 77% complete to 3.0 Å, 66% complete to 2.85 Å, and 52% complete to 2.7 Å.