Table 1. Cryo-EM data collection, refinement and validation statistics.
| Chi-recognised (EMD-10214,PDB 6SJB) |
Chi-intermediate (EMD-10215, PDB 6SJE) |
Chi-unrecognised (EMD-10216,PDB 6SJF) |
Chi-minus (EMDB-10217,PDB 6SJG) |
Chi-minus 2 (EMD-10369, PDB-6T2U) |
Chi-plus 2 (EMD-10370, PDB-6T2V) |
|
|---|---|---|---|---|---|---|
| Data collection and processing | ||||||
| Magnification | 47,755 | 47,755 | 47,755 | 47,710 | 75,000 | 75,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
| Detector | Gatan K2 | Gatan K2 | Gatan K2 | Gatan K2 | Falcon3 (Integrating) | Falcon3 (Integrating) |
| Electron exposure (e–/Å2) | 45 | 45 | 45 | 45 | 75.9 | 75.9 |
| Dose rate (e–/pixel/s) | 5 | 5 | 5 | 7 | 5 | 5 |
| Pixel size (Å) | 1.047 | 1.047 | 1.047 | 1.048 | 1.085 | 1.085 |
| Defocus range (μm) | -1.0 to -3.0 | -1.0 to -3.0 | -1.0 to -3.0 | -1.0 to -2.5 | -1.2 to -2.7 | -1.2 to -2.7 |
| Initial particle images (no.) | 373,476 | 373,476 | 373,476 | 99,545 | 754,150 | 795,810 |
| Final particle images (no.) | 74,496 | 44,320 | 74,273 | 62,812 | 379,790 | 380,912 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
| Map resolution (Å) | 3.7 | 4.1 | 3.9 | 3.8 | 3.6 | 3.8 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | ||||||
| Initial model used (PDB code) | 5LD2 | 6SJB | 5LD2 | 6SJF | 5LD2 | 5LD2 |
| Model resolution (Å) | 3.7 | 4.1 | 3.9 | 3.8 | 3.6 | 3.8 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement program | Phenix 1.12-2829 | Phenix 1.12-2829 | Phenix 1.12-2829 | Phenix 1.12-2829 | Phenix 1.12-2829 | Phenix 1.12-2829 |
| Model to map CC (masked) | 0.80 | 0.77 | 0.78 | 0.73 | 0.71 | 0.73 |
| Map sharpening B factor (Å2) | -50 | -50 | -50 | -50 | -100 | -100 |
| Model composition | ||||||
| Non-hydrogen atoms | 24,115 | 24,115 | 23,826 | 23,826 | 23,826 | 23,826 |
| Protein residues | 2,847 | 2,847 | 2,847 | 2,847 | 2,847 | 2,847 |
| DNA residues | 68 | 68 | 54 | 54 | 54 | 54 |
| B factors (Å2) | ||||||
| Protein | 105 | 118 | 106 | 109 | 94 | 135 |
| DNA | 155 | 172 | 199 | 241 | 147 | 208 |
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.003 | 0.003 | 0.002 | 0.002 | 0.002 | 0.002 |
| Bond angles (°) | 0.56 | 0.58 | 0.52 | 0.54 | 0.46 | 0.43 |
| Validation | ||||||
| Clashscore | 4.4 | 4.3 | 4.4 | 4.3 | 4.5 | 4.6 |
| Poor rotamers (%) | 2.6 | 3.1 | 3.0 | 2.9 | 3.0 | 3.0 |
| Ramachandran plot | ||||||
| Favored (%) | 97.7 | 97.9 | 98.0 | 97.8 | 98.0 | 98.0 |
| Allowed (%) | 2.3 | 2.1 | 2.0 | 2.2 | 2.0 | 2.0 |
| Disallowed (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
FSC = Fourier shell correlation, R.m.s = root means squared, CC = correlation coefficient as calculated by phenix.real_space_refine