Table 1 Cryo-EM data collection and refinement and validation statistics.
| Â | NDH-PQ (EMDB-9990, PDB 6KHJ) | NDH-Fd (EMDB-9989, PDB 6KHI) |
|---|---|---|
Data collection and processing | ||
Magnification | 130,000 | 130,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e−/Å2) | 60 | 60 |
Defocus range (μm) | 0.5–2.5 | 0.5–2.5 |
Pixel size (Ã…) | 1.04 | 1.04 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 434,021 | 276,859 |
Final particle images (no.) | 187,788 | 152,003 |
Map resolution (Ã…) | 3.0 | 3.2 |
     FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.5–4.5 | 2.8–4.4 |
Refinement | ||
Initial model used (PDB code) | 4HEA | NDH-PQ, 5AUI |
Model resolution (Ã…) | 3.0 | 3.2 |
     FSC threshold | 0.5 | 0.5 |
Map sharpening B factor (Å2) | −98 | −106 |
Model composition | ||
     Nonhydrogen atoms | 31,027 | 32,635 |
     Protein residues | 3877 | 4095 |
     Ligands | 20 | 19 |
B factors (Ã…2) | ||
     Protein | 45.0 | 55.6 |
     Ligand | 48.5 | 60.4 |
R.m.s. deviations | ||
     Bond lengths (Å) | 0.007 | 0.006 |
     Bond angles (°) | 0.999 | 0.945 |
Validation | ||
     MolProbity score | 1.86 | 1.92 |
     Clash score | 6.84 | 7.31 |
     Poor rotamers (%) | 0.41 | 0.27 |
Ramachandran plot | ||
     Favored (%) | 92.13 | 91.04 |
     Allowed (%) | 7.85 | 8.94 |
     Disallowed (%) | 0.02 | 0.02 |
