Table 1:
Cryo-EM data collection, refinement and validation statistics
| Pre-GAP complex (EMD-21686, PDB 6JW2) | Post-GAP complex (EMD-21687, PDB 6WJ3) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | 29,000 | 36,000 |
| Voltage (kV) | 300 | 200 |
| Electron exposure (e–/Å2) | 59 | 60.5 |
| Defocus range (μm) | −0.8 to −2.3 | −1.0 to −2.5 |
| Pixel size (Å) | 0.8522 | 1.137 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 1,419,155 | 2,309,565 |
| Final particle images (no.) | 129,553 | 106,659 |
| Map resolution (Å) | 3.2 | 3.9 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 2.6–11 | 3.4–11 |
| Refinement | ||
| Initial model used | PDB 6NZD | PDB 6WJ2 |
| Model resolution (Å) | 3.5 | 4.4 |
| FSC threshold | 0.5 | 0.5 |
| Map sharpening B factor (Å2) | −32.9 | local amplitude scaling |
| Model composition | ||
| Non-hydrogen atoms | 8,909 | 8,912 |
| Protein residues | 1,167 | 1,168 |
| Ligands | 1 GDP; 1 XTPγS (L8S); 1 Mg2+ | 1 GDP; 1 XDP (U3J) |
| B factors (Å2, min / max / avg) | ||
| Protein | 38.89 / 226.58 / 87.85 | 54.13 / 204.34 / 103.71 |
| Ligand | 49.91 / 65.12 / 57.44 | 96.98 / 113.93 / 105.46 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.002 | 0.002 |
| Bond angles (°) | 0.454 | 0.484 |
| Validation | ||
| MolProbity score | 1.91 | 1.76 |
| Clashscore | 3.83 | 7.82 |
| Poor rotamers (%) | 2.81 | 0.00 |
| Ramachandran plot | ||
| Favored (%) | 94.05 | 95.20 |
| Allowed (%) | 5.95 | 4.71 |
| Disallowed (%) | 0.00 | 0.09 |