Table 2.
Cryo-EM data collection, refinement, and validation statistics.
| Fo with bedaquiline (EMDB-21894) (PDB 6WTD) | F1Fo with bedaquiline (EMDB-21895) | |||
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 31,000 | 36,000 | 31,000 | 36,000 |
| Voltage (kV) | 300 | 200 | 300 | 200 |
| Electron exposure (e–/Å2) | 41 | 48 | 41 | 48 |
| Defocus range (μm) | 0.8–2.8 | 0.8–3.0 | 0.8–2.8 | 0.8–3.0 |
| Pixel size (Å) | 1.23 | 1.169 | 1.23 | 1.169 |
| Symmetry imposed | C1 | C1 | ||
| Initial particle images (no.) | 343,518 | 1,063,365 | ||
| Final particle images (no.) | 47,169 | 122,736 | ||
| Map resolution (Å) | 4.2 | 3.9 | ||
| FSC threshold | 0.143 | 0.143 | ||
| Map resolution range (Å) | 3.5–4.5 | 3.0–5.0 | ||
| Refinement | ||||
| Initial model used (PDB code) | 6CP7 | |||
| Model resolution (Å) | 4.2 | |||
| FSC threshold | 0.143 | |||
| Model resolution range (Å) | 4.0–4.1 | |||
| Map sharpening B factor (Å2) | −150 | |||
| Model composition | ||||
| Nonhydrogen atoms | 9139 | |||
| Protein residues | 1233 | |||
| Ligands | 0 | |||
| B factors (Å2) | ||||
| Protein | 106.07 | |||
| Ligand | – | |||
| R.M.S. deviations | ||||
| Bond lengths (Å) | 0.007 | |||
| Bond angles (°) | 1.154 | |||
| Validation | ||||
| MolProbity score | 1.86 | |||
| Clashscore | 7.39 | |||
| Poor rotamers (%) | 0.86 | |||
| Ramachandran plot | ||||
| Favored (%) | 92.78 | |||
| Allowed (%) | 7.22 | |||
| Disallowed (%) | 0.00 | |||