Table 1.
Cryo-EM data collection, model refinement, and validation statistics
| Polymerase module-Mpe1-RNA (PDB: 7ZGP, EMDB: EMD-14710) | Polymerase module-Cft2(S) (PDB: 7ZGQ, EMDB: EMD-14711) | Polymerase module-Mpe1-yPIM-RNA (PDB: 7ZGR, EMDB: EMD-14712) | |
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 105,000 × | 105,000 × | 105,000 × |
| Voltage (kEV) | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 40 | 37 | 40 |
| Defocus range (μm) | −0.5 to −3.1 | −0.5 to −3.1 | −0.5 to −3.1 |
| Pixel size (Å) | 0.83 (eBIC) | 0.86 (LMB) | 0.86 (LMB) |
| Symmetry imposed | C1 | C1 | C1 |
| Initial particle images (no.) | 6,460,073 | 1,946,027 | 13,905,256 |
| Final particle images (no.) | 131,152 | 141,584 | 846,349 |
| Map resolution (Å) | 2.66 | 2.79 | 2.61 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.66 to >10 | 2.79 to >10 | 2.61 to >10 |
| Refinement | |||
| Initial model used | de novo modeling and polymerase module (PDB: 6eoj) | mPSF-PIM (PDB: 6urg) and polymerase module (PDB: 6eoj) | polymerase module-Mpe1-RNA and polymerase module-Cft2(S) |
| Model resolution (Å) | – | – | – |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Model resolution range (Å) | – | – | – |
| Map sharpening B factor (Å2) | −20 | −30 | −40 |
| Model composition | |||
| Non-hydrogen atoms | 14,063 | 13,704 | 14,505 |
| Protein residues | 1,767 | 1,749 | 1,819 |
| Nucleotides | 4 | 0 | 4 |
| Ligands | ZN:2 | ZN:2 | ZN:2 |
| B factors (Å2) | |||
| Protein | not estimated |
not estimated |
not estimated |
| Ligand | |||
| RMS deviations | |||
| Bond lengths (Å) | 0.003 | 0.003 | 0.003 |
| Bond angles (°) | 0.518 | 0.539 | 0.537 |
| Validation | |||
| MolProbity score | 1.97 | 2.39 | 1.93 |
| Clashscore | 9.55 | 11.24 | 8.12 |
| Poor rotamers (%) | 1.15 | 3.25 | 1.30 |
| Ramachandran plot | |||
| Favored (%) | 93.63 | 93.27 | 94.11 |
| Allowed (%) | 6.25 | 6.73 | 5.72 |
| Disallowed (%) | 0.11 | 0.0 | 0.17 |