Table 2 Crystallographic data collection and refinement statistics
MProD48Y/ΔP168 PDB ID 9N6J | MProD48Y/ΔP168-GC373 PDB ID 9N6L | MProD48Y/ΔP168-NMV PDB ID 9N6M | |
|---|---|---|---|
Data collection: | X-ray (in-house) | ||
Diffractometer | Rigaku HighFlux, Eiger R 4 M | ||
Space group | I2 | I2 | I2 |
Wavelength (Å) | 1.5406 | 1.5406 | 1.5406 |
Cell dimensions: | |||
a, b, c (Å) | 52.53, 82.59, 91.32 | 52.77, 81.90, 91.69 | 52.48, 82.47, 91.37 |
α, β, γ (°) | 90, 95.3, 90 | 90, 95.3, 90 | 90, 95.4, 90 |
Resolution (Å) | 61.1–1.85 (1.92–1.85) | 60.9 – 2.20 (2.28 – 2.20) | 61.1–2.00 (2.07–2.00) |
No. reflections unique | 32946 (3264) | 19382 (1906) | 26247 (2629) |
Rmerge | 0.113 (0.702) | 0.082 (0.274) | 0.102 (0.618) |
CC1/2 | 0.919 (0.535) | 0.983 (0.987) | 0.951 (0.670) |
<I/σI> | 13.2 (0.97) | 24.7 (4.7) | 14.2 (1.7) |
Completeness (%) | 99.3 (98.2) | 97.9 (96.3) | 99.9 (99.8) |
Redundancy | 4.5 (4.5) | 4.6 (4.7) | 5.5 (5.3) |
Refinement: | |||
Rwork/Rfree | 0.1897/0.2207 | 0.1806/0.2243 | 0.1779/0.2211 |
B-factors | |||
Protein | 40.1 | 32.3 | 38.9 |
Ligand | N/A | 39.9 | 46.1 |
Water | 41.6 | 31.5 | 37.3 |
Inhibitor occupancy | N/A | 1.00 | 0.68 |
R.M.S. deviations | |||
Bond lengths (Å) | 0.007 | 0.008 | 0.009 |
Bond angles (°) | 0.859 | 0.879 | 0.970 |
All atom clash score | 2.54 | 2.98 | 4.36 |
Ramachandran stats. (%) | |||
Favored | 97.03 | 97.69 | 96.37 |
Allowed | 2.97 | 2.31 | 3.63 |
Outliers | 0 | 0 | 0 |
MProD48Y/ΔP168-PMV PDB ID 9N6N | MProD48Y/ΔP168-ESV PDB ID 9N6P | MProWT-ESV PDB ID 9N6R | |
|---|---|---|---|
Data collection: | X-ray (in-house) | ||
Diffractometer | Rigaku HighFlux, Eiger R 4 M | ||
Space group | I2 | I2 | I2 |
Wavelength (Å) | 1.5406 | 1.5406 | 1.5406 |
Cell dimensions: | |||
a, b, c (Å) | 52.34, 82.37, 91.09 | 52.26, 83.33, 91.00 | 52.02, 83.30, 90.97 |
α, β, γ (°) | 90, 95.4, 90 | 90, 95.5, 90 | 90, 95.4, 90 |
Resolution (Å) | 61.0–1.85 (1.92–1.85) | 61.3–1.90 (1.97–1.90) | 61.3–1.70 (1.76–1.70) |
No. reflections unique | 32821 (3285) | 29235 (2850) | 42304 (4186) |
Rmerge | 0.102 (0.569) | 0.115 (0.544) | 0.071 (0.610) |
CC1/2 | 0.954 (0.674) | 0.940 (0.774) | 0.968 (0.722) |
<I/σI> | 18.9 (1.5) | 13.2 (1.9) | 22.3 (1.7) |
Completeness (%) | 99.9 (98.8) | 95.4 (93.0) | 99.6 (98.4) |
Redundancy | 4.3 (3.3) | 4.7 (4.8) | 5.4 (5.2) |
Refinement: | |||
Rwork/Rfree | 0.1737/0.2179 | 0.1679/0.1993 | 0.1708/0.2020 |
B-factors | |||
Protein | 41.2 | 37.9 | 34.1 |
Ligand | 59.7 | 37.5 | 30.0 |
Water | 41.6 | 41.2 | 37.6 |
Inhibitor occupancy | 0.65 | 0.75 | 1.00 |
R.M.S. deviations | |||
Bond lengths (Å) | 0.011 | 0.017 | 0.017 |
Bond angles (°) | 1.197 | 1.462 | 1.474 |
All atom clash score | 5.44 | 4.02 | 2.12 |
Ramachandran stats. (%) | |||
Favored | 97.36 | 97.99 | 97.33 |
Allowed | 2.64 | 2.01 | 2.67 |
Outliers | 0 | 0 | 0 |
