Table 2.
Statistics of the single-particle cryo-EM structure of the oxidized chloroplast ATP synthase of Spinacia oleracea.
| Chloroplast ATP synthase of Spinacia oleracea in iodosobenzoate (IBZ) | |||
|---|---|---|---|
| O1 | O2 | O3 | |
| (EMD-21264, EMD-21265) | (EMD-21262, EMD-21263) | (EMD-21241) | |
| (PDB codes: 6VOH, 6VOI) | (PDB codes: 6VOF, 6VOG) | (PDB codes: 6VMG) | |
| Data collection and processing | |||
| Magnification | 48,077× | ||
| Voltage (kV) | 300 | ||
| Electron exposure (e−/Å2) | 44.4 | ||
| Defocus range (μm) | −1.5 to −4.0 | ||
| Pixel size (Å) | 1.04 | ||
| Symmetry imposed | C1 | ||
| Initial particle images (no.) | 552,893 | ||
| Final particle images (no.) | 304,879 | 114,542 | 29,090 |
| Map resolution (Å) | 4.16 (4.03) | 4.51 (4.35) | 6.46 |
| FSC threshold | |||
| Refinement | |||
| Initial model used (PDB code) | 6FKF | 6FKH | 6FKI |
| Model resolution (Å) | 4.1 (3.9) | 4.4 (4.3) | 6.6 |
| FSC threshold of 0.143 | |||
| Cross correlation | |||
| Masked | 0.728 (0.752) | 0.774 (0.824) | 0.711 |
| Volume | 0.712 (0.734) | 0.773 (0.821) | 0.696 |
| Map sharpening b factor (Å2) | −211.95 (−203.09) | −179.39 (−232.12) | −304.57 |
| Model composition | |||
| Non-hydrogen atoms | 39,159 (27,497) | 35,182 (27,137) | 25,375 |
| Protein residues | 5193 (3575) | 5175 (3563) | 5170 |
| Ligands | |||
| ATP | 4 | 4 | 0 |
| ADP | 1 | 1 | 0 |
| B factors (Å2) | |||
| Protein | 84.67 (64.35) | 144.23 (158.45) | 222.15 |
| Ligands | 68.15 (55.87) | 119.07 (142.64) | |
| RMS deviations | |||
| Bond lengths (Å) | 0.005 (0.005) | 0.007 (0.006) | 0.006 |
| Bond angles (°) | 0.941 (0.881) | 0.983 (1.025) | 0.970 |
| Validation | |||
| MolProbity score | 2.14 (2.12) | 2.19 (2.20) | 2.05 |
| Clashscore | 14.08 (13.35) | 15.13 (15.24) | 9.65 |
| Poor rotamers (%) | 0.49 (0.24) | 0.76 (0.49) | 0.00 |
| Ramachandran plot | |||
| Favored (%) | 92.02 (91.96) | 91.63 (91.11) | 90.31 |
| Allowed (%) | 7.68 (7.73) | 8.32 (8.80) | 9.60 |
| Disallowed (%) | 0.29 (0.31) | 0.06 (0.08) | 0.10 |
Values in the parentheses are the refinement statistics for the F1 region.