Table 1.
Cryo-EM data collection, refinement and validation statistics
| OAD-MTD array (apo state) | Free OAD (apo state) | ||||
|---|---|---|---|---|---|
| Data collection and processing | Dataset 1 | Dataset 2 | Dataset 3 | Dataset 4 | |
| Magnification | ×165,000 | ×165,000 | ×105,000 | ×105,000 | |
| Voltage (kV) | 300 | 300 | 300 | 300 | |
| Electron exposure (e−/Å2) | 53.3 | 53.3 | 53.3 | 53.3 | |
| Defocus range (μm) | −1.0 to −2.0 | −1.0 to −2.0 | −1.5 to −2.5 | −1.5 to −2.5 | |
| Pixel size (Å) | 0.822 | 0.822 | 1.333 | 1.333 | |
| Symmetry imposed | C1 | C1 | C1 | C1 | |
| Initial particle images (no.) | 207,795 | 616,864 | 2,022,385 | 883,738 | |
| Final particle images (no.) | 6,895 | 7,288 | 188,989 | 209,656 | |
| Merged particles images (no.) | 268,712 | 209,656 | |||
| Final particles for refinement (no.) | 191,776 | 76,936 | 209,656 | ||
| OAD-PF MTBS-1 | OAD-PF MTBS-2 | Preparallel OAD | |||
| (EMD-22677) | (EMD-22679) | (EMD-22840) | |||
| (PDB 7K58) | (PDB 7K5B) | (PDB 7KEK) | |||
| Map resolution (Å) | 3.5 | 4.5 | 8.0 | ||
| FSC threshold | 0.143 | 0.143 | 0.143 | ||
| Map resolution range (Å) | 2.8-10 | 3.8-6.0 | 5.0-12 | ||
| Refinement | |||||
| Initial model used | Ab initio | Ab initio | Ab initio | Ab initio | |
| Model resolution (Å) | 3.5 | 3.96 | 3.82 | 3.83 | |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | |
| Model resolution range (Å) | 3.5-7.0 | ||||
| Map sharpening B factor (Å2) | −80 | −80 | −80 | −80 | |
| Model composition | Entire | α-Motor | β-Motor | γ-Motor | |
| Nonhydrogen atoms | 201,509 | 21,493 | 21,535 | 23,540 | |
| Protein residues | 26,111 | 2,671 | 2,661 | 2,924 | |
| Ligands | ATP/ADP/ Mg2+ (3/6/9); | ATP/ADP/ Mg2+ (1/2/3) | ATP/ADP/ Mg2+ (1/2/3) | ATP/ADP/ Mg2+ (1/2/3) | |
| GTP/GDP/Mg2+ (12/12/12) | |||||
| B factors (Å2) | |||||
| Protein | 145.912 | 207.098 | 214.995 | 230.879 | |
| Ligand | |||||
| R.m.s. deviations | |||||
| Bond lengths (Å) | 0.0030 | 0.0031 | 0.0027 | 0.0027 | |
| Bond angles (°) | 1.3386 | 1.3286 | 1.2985 | 1.3010 | |
| Validation | |||||
| MolProbity score | 2.00 (100th) | 1.90 (100th) | 1.87 (100th) | 1.71 (100th) | |
| Clashscore | 4.68 (100th) | 4.56 (100th) | 4.75 (100th) | 3.92 (100th) | |
| Poor rotamers (%) | 2.21 | 2.57 | 3.92 | 2.58 | |
| Ramachandran plot | |||||
| Favored (%) | 91.78 | 94.51 | 95.54 | 94.09 | |
| Allowed (%) | 7.31 | 5.08 | 4.20 | 5.36 | |
| Disallowed (%) | 0.91 | 0.41 | 0.26 | 0.55 | |