Table 1.
Data collection and refinement statistics. Calculated using Phenix [13]. R-work = Σ |fo| − |fc| / Σ |fo|, fo and fc are observed and calculated structure factors. Statistics for the highest-resolution shell are shown in parentheses.
| Ligand | Native | ZAI | ZA | |||
|---|---|---|---|---|---|---|
| pdb code | 1qo9 | 6xys | 1qon | 6xyu | 1dx4 | 6xyy |
| Software | ||||||
| Integration | DENZO | XDS | DENZO | XDS | DENZO | |
| Scaling | SCALEPACK | XSCALE | SCALEPACK | XSCALE | SCALEPACK | |
| Refinement | CNS | Phenix | CNS | Phenix | CNS | Phenix |
| Model building | O | Coot | O | Coot | O | Coot |
| Data Collection | ||||||
| X-ray source—beamline | Elettra, Trieste, XRD | Elettra, Trieste, XRD | NSLS, BNL, X12C | |||
| wavelength (Å) | 1.0 | 1.0 | 0.98 | |||
| Resolution range (Å) | 29.83–2.7 | 30.94– 2.45 | 26.54–2.707 | 40.82–2.51 | 29.78–2.7 | |
| (highest-resolution shell) | (2.796–2.7) | (2.543–2.455) | (2.804–2.707) | (2.6–2.51) | (2.796–2.7) | |
| space group, mol/AU | P43212, 1 | P43212, 1 | P43212, 1 | P43212, 1 | P43212, 1 | |
| unit cell parameters (Å) | 94.3 94.3 159.0 90 90 90 |
94.6 94.6 159.0 90 90 90 |
94.9 94.9 160.0 90 90 90 |
94.9 94.9 160.0 90 90 90 |
95.8 95.8 162.0 90 90 90 |
|
| Total reflections | na | 161402 (9870) | na | 70404 (6919) | na | |
| Unique reflections | 20199 (1956) | 26803 (2542) | 19963 (1998) | 24909 (2458) | 20596 (1809) | |
| Multiplicity | na | 6.0 (3.9) | na | 2.8 (2.8) | na | |
| Completeness (%) | 98.95 (98.79) | 98.54 (95.29) | 96.58 (98.71) | 96.64 (98.40) | 95.98 (86.67) | |
| Mean I/σ (I) | 33.5 (5.8) | 20.7 (3.3) | 15.5 (2.4) | 10.97 (1.68) | 24.3 (3.2) | |
| Wilson B-factor | 45.34 | 51.47 | 49.70 | 52.05 | 50.19 | |
| R-merge | na | 0.0487 (0.335) | na | 0.0635 (0.519) | na | |
| R-meas | 0.05 (0.161) | 0.0524 (0.387) | 0.060 (0.254) | 0.0766 (0.638) | 0.038 (0.274) | |
| R-pim | na | 0.0184 (0.1848) | na | 0.0412 (0.358) | na | |
| CC1/2 | na | 0.999 (0.939) | na | 0.997 (0.763) | na | |
| CC* | na | 1 (0.984) | na | 0.999 (0.93) | na | |
| Refinement Statistics | ||||||
| Reflections used | 20196 (1956) | 26739 (2530) | 19930 (1996) | 24876 (2457) | 20578 (1807) | 20577 (1807) |
| Reflections for R-free | 1990 (176) | 1338 (126) | 1704 (152) | 870 (86) | 2030 (193) | 2030 (193) |
| R-work | 0.2728 (0.4117) | 0.2297 (0.3959) | 0.2325 (0.3431) | 0.1857 (0.3252) | 0.2241 (0.3180) | 0.1711 (0.2461) |
| R-free | 0.2701 (0.4481) | 0.2950 (0.5239) | 0.2604 (0.3615) | 0.2522 (0.4266) | 0.2595 (0.3321) | 0.2335 (0.3270) |
| Number of non-H atoms | 4479 | 4398 | 4486 | 4447 | 4413 | 4483 |
| macromolecule | 4273 | 4239 | 4258 | 4230 | 4231 | 4242 |
| ligands | 75 | 65 | 89 | 63 | 91 | 97 |
| solvent | 131 | 94 | 139 | 154 | 97 | 144 |
| Protein residues | 540 | 542 | 686 | 542 | 537 | 537 |
| RMSD (bonds; Å) | 0.010 | 0.008 | 0.011 | 0.008 | 0.008 | 0.008 |
| RMSD (angles; deg) | 1.81 | 1.05 | 1.54 | 0.96 | 1.41 | 0.90 |
| Ramachandran favored (%) | 77.99 | 90.96 | 88.81 | 94.93 | 88.93 | 95.12 |
| Ramachandran allowed (%) | 16.04 | 8.10 | 9.33 | 4.50 | 9.38 | 4.50 |
| Ramachandran outliers (%) | 5.97 | 0.94 | 1.87 | 0.56 | 1.69 | 0.38 |
| Rotamer outliers (%) | 10.34 | 0.22 | 7.16 | 0.00 | 6.28 | 0.22 |
| Clashscore | 64.63 | 18.47 | 35.07 | 10.40 | 28.62 | 7.45 |
| Average B-factor (Å2) | 58.32 | 79.57 | 54.32 | 66.71 | 50.47 | 56.87 |
| macromolecules (Å2) | 58.43 | 79.61 | 54.02 | 66.59 | 50.15 | 56.43 |
| ligands (Å2) | 85.59 | 102.26 | 84.26 | 85.23 | 75.02 | 85.34 |
| solvent (Å2) | 39.15 | 61.86 | 44.27 | 62.47 | 40.67 | 50.57 |
| Number of TLS groups | - | 5 | - | 3 | - | 4 |