Table 2.
Data collection and refinement statistics
| Data set | Apo | + NADH | + LG, NADH | + Sorbose, NADH |
|---|---|---|---|---|
| Data collection | ||||
| Beamline | AR-NE3A (KEK-PF) | AR-NW12A (KEK-PF) | BL1A (KEK-PF) | BL26B1 (SPring-8) |
| Space group | P43212 | P21 | P21 | P21 |
| Unit cell | a = b = 95.6 c = 120.8 | a = 80.7 | a = 76.7 | a = 80.2 |
| Dimensions (Å) and angles (°) | b = 93.8 | b = 92.4 | b = 93.5 | |
| c = 101.0 | c = 100.6 | c = 100.9 | ||
| β = 101.0 | β = 104.5 | β = 101.4 | ||
| Mole/ASUa | 2 | 4 | 4 | 4 |
| Resolution (Å)b | 50.0–1.80 (1.83–1.80) | 50.0–1.90 (1.93–1.90) | 50.0–2.40 (2.44–2.40) | 50.0–1.90 (1.93–1.90) |
| Total reflections | 1,050,924 | 407,615 | 170,900 | 431,229 |
| Unique reflectionsb | 74,076 (3,610) | 114,689 (5,628) | 51,934 (2590) | 114,792 (5696) |
| Completeness (%)b | 99.9 (100.0) | 98.7 (97.2) | 99.5 (99.7) | 100.0 (99.9) |
| Redundancyb | 14.2 (13.2) | 3.6 (3.3) | 3.3 (3.4) | 3.8 (3.7) |
| Mean I/σ(I) b | 35.4 (3.4) | 11.4 (1.4) | 16.1 (2.4) | 13.8 (1.7) |
| Rmerge (%)b | 9.3 (69.4) | 10.4 (77.7) | 8.3 (52.0) | 10.3 (72.0) |
| CC1/2a | (0.974) | (0.903) | (0.959) | (0.936) |
| Wilson B-factor (Å2) | 27.84 | 23.47 | 63.79 | 28.60 |
| Refinement | ||||
| Resolution (Å) | 38.28–1.80 | 36.53–1.90 | 34.84–2.41 | 49.49–1.90 |
| No. of reflections | 70,139 | 109,019 | 49,298 | 108,882 |
| Rwork/Rfree (%) | 16.7/20.2 | 16.9/20.4 | 21.5/29.7 | 16.6/20.7 |
| No. of atoms (protein/heterogen/solvent) | 6,350 | 12,439 | 11,518 | 12,478 |
| r.m.s.d. from ideal values | ||||
| Bond lengths (Å) | 0.013 | 0.010 | 0.008 | 0.010 |
| Bond angles (°) | 1.555 | 1.423 | 1.248 | 1.433 |
| No. of solvents and ligands | ||||
| Waters | 484 | 749 | 61 | 767 |
| SO4 | 3 | |||
| MES | 2 | |||
| NADHc | 4 (A, B, C, D) | 3 (A*, B**, C**) | 4 (A*, B*, C*, D*) | |
| Substratec | LG × 2 (A, D) | l-Sorbose × 4 (A, B, C, D) | ||
| Average B-factors (Å2) (chain A/B/C/D) | ||||
| Protein | 28.6/28.4 | 22.6/24.3/25.6/23.5 | 53.1/62.1/72.1/77.8 | 27.1/29.2/30.1/30.8 |
| NADH | 23.0/25.3/28.3/24.8 | 48.3/58.5/65.4/– | 25.0/29.2/30.0/31.1 | |
| Substrate | 62.5/−/−/65.0 | 25.4/26.7/25.7/26.1 | ||
| Solvents | 35.1 | 31.3 | 49.7 | 36.5 |
| Ramachandran plot (%) | ||||
| Favored | 98.1 | 98.2 | 93.7 | 98.0 |
| Allowed | 1.9 | 1.8 | 5.5 | 2.0 |
| Outlier | 0.0 | 0.0 | 0.8 | 0.1 |
| PDB code | 6A3F | 6A3G | 6A3I | 6A3J |
a Number of molecules in the asymmetric unit is shown.
b Values in parentheses are for the highest resolution shell.
c Modeled chains are indicated in parentheses. For NADH, a single asterisk indicates that the nicotinamide moiety was not modeled. Double asterisks indicate that both the nicotinamide and adenine moieties were not modeled.