Table 1.
Data collection and processing.
| Extended (Fe2+–NAD+–CoA) | Compact (Fe2+–NADH) | |||
|---|---|---|---|---|
| Data collection | ||||
| Microscope–camera | Talos Arctica–K2 summit | Talos Arctica–K2 summit | ||
| Voltage (kV) | 200 | 200 | ||
| Magnification | 36,000 | 36,000 | ||
| Electron exposure (e− per Å2) | 0.77 | 0.77 | ||
| Pixel size (Å) | 1.13 | 1.13 | ||
| Decofus range (um) | 0.4 – 2.4 | 0.4 – 2.4 | ||
| Processing | Helical reconstruction | Single-particle analysis | Helical reconstruction | Single-particle analysis |
| Symmetry imposed |
C1 Rise 56.5 Å, Twist 164.4° |
C1 C2 |
C1 Rise 34.7 Å, Twist 154.5° |
C1 |
| Initial particle images (no.) | 821,557 | 1,236,367 | 227,537 | 599,988 |
| Final particle images (no.) | 203,288 | 138,927 | 98,677 | 226,646 |
| Map resolution (Å)–(FSC threshold model) | 3.8–(0.143) | 3.4–(0.143) | 5–(0.143) | 3.9–(0.143) |
| Refinement and validation | ||||
| Map sharpening (B-factor) (Å−2) | 121.41 | 82.58 | 246.65 | 206.89 |
| Model composition | ||||
| No. of chains | 6 | 6 | ||
| Atoms (no.) | 39,781 | 39,760 | ||
| Residues (no.) | 2576 | 2578 | ||
| Ligands (no.) | Fe2+ (2)–NAD+ (4) | Fe2+ (2)–NADH (2) | ||
| Bond lengths (Å) | 0.011 | 0.006 | ||
| Bond angles (°) | 0.989 | 1.587 | ||
| Ramachandran favored % | 87.46 | 85.02 | ||
| Ramachandran allowed % | 12.54 | 14.05 | ||
| Ramachandran outliers % | 0.00 | 0.93 | ||
| Rotamers outliers % | 1.45 | 3.67 | ||
| MolProbity score | 2.11 | 2.59 | ||
| Clashscore | 6.89 | 9.43 | ||
| CC (mask) | 0.82 | 0.78 | ||
| CC (box) | 0.83 | 0.77 | ||
| CC (peaks) | 0.73 | 0.60 | ||
| CC (volume) | 0.82 | 0.79 | ||
| Mean CC for ligands | 0.76 | 0.71 | ||