Table 1.
Data collection, processing, and refinement statistics
| Deposition Id | EMD-23569 |
EMD-23615 |
EMD-23627 |
|---|---|---|---|
| PDB: 7LXB | PDB: 7M18 | PDB: 7M20 | |
| Data collection | |||
| Magnification | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 |
| Total dose (e−/Å) | 66 | 66 | 66 |
| Frame rate | 4 frames/s | 4 frames/s | 4 frames/s |
| Defocus range (μm) | −0.6 to −2.6 | −0.6 to −2.6 | −0.6 to −2.6 |
| Pixel size | 1.06 | 1.06 | 1.06 |
| Data processing | |||
| Symmetry | C8 | C8 | C9 |
| Initial particle number | 40,746 | 35,113 | 35,113 |
| Final particle number | 31,098 | 18,899 | 14,468 |
| Resolution (Å) | 3.3 | 3.4 | 3.8 |
| Fourier shell correlation threshold | 0.143 | 0.143 | 0.143 |
| Refinement | |||
| Map sharpening b-factor (Å2) | −90 | −90 | −150 |
| Model composition | |||
| Nonhydrogen atoms | 54,280 | 54,064 | 60,705 |
| Protein residues | 6928 | 6904 | 7785 |
| Ligands | 24 | 24 | 27 |
| B-factors (Å2) | |||
| Protein | 125.8 | 118.6 | 161.6 |
| Ligand | 93.4 | 84.6 | 129.1 |
| Nucleotide (GTP/GDP) | 119.0/113.9 | 99.0/95.2 | 145.0/135.0 |
| RMSD | |||
| Bond length (Å) | 0 | 0 | 0 |
| Bond angles (°) | 0 | 0 | 0 |
| Validation | |||
| Model-to-map fit CC protein | 0.75 | 0.73 | 0.76 |
| Model-to-map fit CC ligand | 0.77 | 0.74 | 0.69 |
| Model-to-map fit CC nucleotide (GTP/GDP) | 0.81/0.76 | 0.84/0.72 | 0.77/0.72 |
| Molprobity score | 2.45 | 2.72 | 2.75 |
| Clashscore | 22 | 21 | 30 |
| Side-chain outliers (%) | 0.9 | 0.8 | 3.1 |
| Ramachandran plot | |||
| Favored (%) | 87.2 | 82.9 | 83.1 |
| Allowed (%) | 12.2 | 16.8 | 16.6 |
| Disallowed (%) | 0.6 | 0.3 | 0.3 |