Table 2 Cryo-EM data collection, refinement, and validation statistics.
From: Bedaquiline inhibits the yeast and human mitochondrial ATP synthases
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 | |||
