Table 1.
Cryo-EM data collection, model refinement, and validation statistics
| High-resolution EMDB:EMD-12165 (PDB: 7BFP) | Medium-resolution (ESRF1) EMDB:EMD-12166 (PDB: 7BFQ) | INTS4-focused EMDB:EMD-12164 (PDB: 7BFQ) | CTD2-focused EMDB:EMD-12163 (PDB: 7BFQ) | |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 165,000 | 165,000 | 165,000 | 165,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 42–46.8 | 46.8 | 46.8 | 46.8 |
| Defocus range (μm) | −0.5 to −3.0 | −0.5 to −3.0 | −0.5 to −3.0 | −0.5 to −3.0 |
| Pixel size (Å) | 0.83 | 0.83 | 0.83 | 0.83 |
| Symmetry imposed | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 9,124,445 | 1,017,432 | 1,017,432 | 1,017,432 |
| Final particle images (no.) | 26358 | 21,866 | 21,235 | 19,938 |
| Map resolution (Å) | 3. | 4.1 | 6.5 | 6.5 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.4–5 | 4–6 | 5–9 | 5–9 |
| Refinement | ||||
| Model resolution (Å) | 4.1 (average) | |||
| FSC threshold | 0.5 | |||
| FSCaverage(Refmac) | 0.7 (at 3.5 Å) | |||
| Model resolution range (Å) | 3.4–5 | |||
| Map sharpening B factor (Å2) | −50 | |||
| Model composition | ||||
| Non-hydrogen atoms | 10,668 | |||
| Protein residues | 1340 | |||
| B factors (Å2) | ||||
| Protein | 148 | |||
| RMSDs | ||||
| Bond lengths (Å) | 0.01 | |||
| Bond angles (°) | 0.16 | |||
| Model validation | ||||
| MolProbity score | 2.2 | |||
| Clashscore | 8.7 | |||
| Poor rotamers (%) | 2.4 | |||
| Ramachandran plot | ||||
| Favored (%) | 93.1 | |||
| Allowed (%) | 6.5 | |||
| Disallowed (%) | 0.4 | |||