Table 1.
Cryo-EM data collection, refinement and validation statistics
| Map 1 global (EMD-13002, PDB 7ONU) | Map 2 PRORP focused (EMD-13002, PDB 7ONU) | |
|---|---|---|
| Data collection and processing | ||
| Magnification | ×105,000 | ×105,000 |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e−/Å2) | 39.6 | 39.6 |
| Defocus range (μm) | 0.2–2.5 | 0.2–2.5 |
| Pixel size (Å) | 0.834 | 0.834 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 6,150,677 | 6,150,677 |
| Final particle images (no.) | 88,081 | 88,081 |
| Map resolution (Å) | 3.0 | 3.1 |
| FSC threshold | 0.143 | 0.143 |
| Map resolution range (Å) | 4.7–2.7 | 4.7–3.0 |
| Map sharpening B factors (Å2) | −61.4 | −72.3 |
| Refinement | ||
| Cryo-EM map used | Composite map from map 1 and 2 | |
| Initial models used (PDB codes) | 1U7T, 5NFJ, 4XGL, 3TUP | |
| Model resolution (Å) | 3.0 | |
| FSC threshold | 0.5 | |
| Model composition | ||
| Nonhydrogen atoms | 15,088 | |
| Protein/nucleotide residues | 1,764/66 | |
| Ligands | ZN:1, MG:1, NAI:4 | |
| B factors (Å2), min./max./mean | ||
| Protein | 22.58/70.49/36.85 | |
| Nucleotide | 38.29/70.72/48.75 | |
| Ligand | 33.68/49.62/37.59 | |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.004 | |
| Bond angles (°) | 0.941 | |
| Validation | ||
| MolProbity score | 1.30 | |
| Clashscore | 3.39 | |
| Rotamer outliers (%) | 0.07 | |
| Ramachandran plot | ||
| Favored (%) | 97.60 | |
| Allowed (%) | 2.40 | |
| Disallowed (%) | 0.00 | |