Table 1.
Statistics of the single-particle cryo-EM structure of the reduced chloroplast ATP synthase of Spinacia oleracea.
| Chloroplast ATP synthase of Spinacia oleracea in dithiothreitol (DTT) |
|||
|---|---|---|---|
| R1 | R2 | R3 | |
| (EMD-21270, EMD-21271) | (EMD-21268, EMD-21269) | (EMD-21266, EMD-21267) | |
| (PDB codes: 6VON, 6VOO) | (PDB codes: 6VOL, 6VOM) | (PDB codes: 6VOJ, 6VOK) | |
| Data collection and processing | |||
| Magnification | 130,000× | ||
| Voltage (kV) | 300 | ||
| Electron exposure (e−/Å2) | 49 | ||
| Defocus range (μm) | −1.0 to −2.8 | ||
| Pixel size (Å) | 1.053 | ||
| Symmetry imposed | C1 | ||
| Initial particle images (no.) | 108,691 | ||
| Final particle images (no.) | 46,180 | 29,667 | 10,264 |
| Map resolution (Å) | 3.35 (3.05) | 4.06 (3.60) | 4.34 (3.85) |
| FSC threshold | |||
| Refinement | |||
| Initial model used (PDB code) | 6FKF | 6FKH | 6FKI |
| Model resolution (Å) | 3.3 (3.1) | 3.9 (3.6) | 4.2 (3.7) |
| FSC threshold of 0.143 | |||
| Cross correlation | |||
| Masked | 0.718 (0.760) | 0.705 (0.702) | 0.668 (0.708) |
| Volume | 0.704 (0.747) | 0.718 (0.702) | 0.676 (0.713) |
| Map sharpening b factor (Å2) | −50.65 (−34.10) | −64.42 (−61.15) | −76.98 (−60.57) |
| Model composition | |||
| Non-hydrogen atoms | 39,163 (27,551) | 38,991 (27,492) | 39,155 (27,512) |
| Protein residues | 5186 (3574) | 5165 (3566) | 5185 (3569) |
| Ligands | |||
| ATP | 4 | 4 | 4 |
| ADP | 2 | 2 | 2 |
| Tentoxin | 1 | 1 | 1 |
| B factors (Å2) | |||
| Protein | 52.25 (58.02) | 33.99 (45.03) | 63.72 (40.88) |
| Ligands | 26.06 (44.20) | 22.88 (34.80) | 30.79 (26.45) |
| RMS deviations | |||
| Bond lengths (Å) | 0.005 (0.006) | 0.005 (0.005) | 0.005 (0.007) |
| Bond angles (°) | 0.861 (0.787) | 0.848 (0.862) | 0.899 (0.974) |
| Validation | |||
| MolProbity score | 1.85 (1.90) | 1.98 (1.98) | 1.92 (2.03) |
| Clashscore | 8.30 (8.99) | 12.48 (11.60) | 9.88 (10.75) |
| Poor rotamers (%) | 0.05 (0.03) | 0.12 (0.10) | 0.34 (0.51) |
| Ramachandran plot | |||
| Favored (%) | 94.08 (93.64) | 94.66 (93.88) | 94.04 (92.31) |
| Allowed (%) | 5.82 (6.21) | 5.20 (5.95) | 5.88 (7.58) |
| Disallowed (%) | 0.10 (0.14) | 0.14 (0.17) | 0.08 (0.11) |
Values in the parentheses are the refinement statistics for the F1 region.