Table 3.
Statistics of the single-particle cryo-EM structure of the control chloroplast ATP synthase of Spinacia oleracea.
| Chloroplast ATP synthase of Spinacia oleracea | |||
|---|---|---|---|
| C1 | C2 | C3 | |
| (EMD-21239, EMD-21240) | (EMD-21238) | (EMD-21235) | |
| (PDB codes: 6VMB, 6VMD) | (PDB codes: 6VM4) | (PDB codes: 6VM1) | |
| Data collection and processing | |||
| Magnification | 48,077× | ||
| Voltage (kV) | 300 | ||
| Electron exposure (e−/Å2) | 43.5 | ||
| Defocus range (μm) | −1.5 to −4.0 | ||
| Pixel size (Å) | 1.04 | ||
| Symmetry imposed | C1 | ||
| Initial particle images (no.) | 208,371 | ||
| Final particle images (no.) | 127,760 | 26,291 | 13,947 |
| Map resolution (Å) | 5.23 (4.53) | 7.08 | 7.90 |
| FSC threshold | |||
| Refinement | |||
| Initial model used (PDB code) | 6FKF | 6FKH | 6FKI |
| Model resolution (Å) | 6.5 (4.5) | 7.2 | 7.9 |
| FSC threshold of 0.143 | |||
| Cross correlation | |||
| Masked | 0.764 (0.841) | 0.787 | 0.786 |
| Volume | 0.753 (0.836) | 0.764 | 0.768 |
| Map sharpening b factor (Å2) | −187.09 (−195.21) | −269.31 | −507.69 |
| Model composition | |||
| Non-hydrogen atoms | 35,401 (27,501) | 25,445 | 25,331 |
| Protein residues | 5194 (3576) | 5184 | 5161 |
| Ligands | |||
| ATP | 4 | 0 | 0 |
| ADP | 1 | 0 | 0 |
| B factors (Å2) | |||
| Protein | 306.88 (130.00) | 376.31 | 286.00 |
| Ligands | 233.70 (101.89) | ||
| RMS deviations | |||
| Bond lengths (Å) | 0.006 (0.008) | 0.007 | 0.007 |
| Bond angles (°) | 1.064 (1.097) | 0.948 | 1.054 |
| Validation | |||
| MolProbity score | 2.01 (2.18) | 1.98 | 2.27 |
| Clashscore | 10.54 (12.90) | 7.94 | 12.03 |
| Poor rotamers (%) | 0.51 (0.82) | 0.00 | 0.00 |
| Ramachandran plot | |||
| Favored (%) | 92.59 (89.74) | 90.02 | 84.46 |
| Allowed (%) | 7.23 (10.12) | 9.90 | 15.42 |
| Disallowed (%) | 0.18 (0.14) | 0.08 | 0.12 |
Values in the parentheses are the refinement statistics for the F1 region.