Table 2.
Apo | Holo-1 | Holo-2 | Holo-3 | Ternary complex | |
---|---|---|---|---|---|
PDB entry | 5EEB | 5F2C | 5EUY | 5EXF | 5EK6 |
Data collection | |||||
Space group | P 21 21 2 | P 21 21 2 | P 21 21 2 | P 21 21 2 | P 21 21 2 |
Cell dimensions | |||||
a (Å) | 184.24 | 185.36 | 184.77 | 185.59 | 183.80 |
b (Å) | 207.23 | 208.30 | 208.05 | 208.72 | 207.85 |
c (Å) | 164.96 | 163.81 | 165.40 | 164.75 | 166.44 |
Temperature (K) | 100 | 100 | 100 | 100 | 100 |
Wavelength (Å) | 0.984 | 0.800 | 0.970 | 1.00 | 0.972 |
Crystal-to-detector distance (mm) | 168.0 | 300.0 | 363.1 | 300.0 | 386.9 |
Oscillation range (°) | 1.0 | 0.5 | 0.1 | 0.5 | 0.1 |
Number of frames | 197 | 720 | 1120 | 720 | 1450 |
Resolution (°) | 29.77–3.04 | 29.15–1.90 | 59.06–2.06 | 90.97–2.19 | 59.14–2.66 |
Completeness (%) | 98.9 (85.0) | 99.8 (99.0) | 99.1 (99.0) | 98.2 (97.9) | 99.34 (100) |
R-merge | 0.27 (0.76) | 0.07 (0.33) | 0.10 (0.77) | 0.19 (0.73) | 0.17 (0.77) |
I/σ | 7.7 (2.3) | 13.4 (1.6) | 8.3 (1.6) | 5.3 (1.7) | 7.3 (1.8) |
Redundancy | 7.4 | 4.0 | 4.1 | 4.9 | 5.4 |
Refinement | |||||
R work/R free | 0.202/0.256 | 0.184/0.218 | 0.196/0.233 | 0.206/0.245 | 0.189/0.240 |
Wilson B-factor (Å2) | 43.5 | 25.0 | 35.3 | 22.0 | 42.0 |
Number of atoms | |||||
All | 30043 | 34276 | 33663 | 33881 | 30912 |
(i) Protein | 30043 | 30690 | 30355 | 30382 | 30054 |
(ii) NADP+ | — | 396 | 408 | 384 | 384 |
(iii) Isobut. | — | — | — | — | 30 |
(iv) Glycerol | — | 6 | — | 6 | — |
(v) Water molecules | — | 3184 | 2900 | 3109 | 444 |
Average B, all atoms (Å2) | 35.0 | 28.0 | 37.0 | 27.0 | 40.0 |
RMS deviations | |||||
(i) Bond lengths | 0.010 | 0.008 | 0.008 | 0.008 | 0.011 |
(ii) Bond angles | 1.274 | 1.021 | 1.058 | 1.071 | 1.197 |
Ramachandran plot | |||||
Most favorable (%) | 97.43 | 97.34 | 96.80 | 96.24 | 95.41 |
Allowed (%) | 2.47 | 2.45 | 2.86 | 3.40 | 3.94 |
Outliers (%) | 0.1 | 0.21 | 0.34 | 0.37 | 0.65 |