Extended Table 1: Summary of cryoEM data collection and refinement.
To obtain the best model-map fit, ADP real space refinement was applied in PHENIX. The B factors increase significantly during ADP real-space refinement. These numbers do not represent the physical meaning of B factors as them in crystallography25.
| Class 1 (EMDB-20840 (PDB 6UPK) |
Class 2 (EMDB-20841) (PDB 6UPL) |
||
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 105,000 | ||
| Voltage (kV) | 300 | ||
| Electron exposure (e-/Å2) | 70 | ||
| Defocus range (μm) | 1.5-2.5 | ||
| Pixel size (Å) | 1.0961 | ||
| Symmetry imposed | C1 | C1 | |
| Initial particle images (no.) | 162,798 | ||
| Final particle images (no.) | 16,784 | 4212 | |
| Map resolution (Å) | 4.9 | 7.4 | |
| FSC threshold | 0.143 | ||
| Map resolution range (Å) | 4.9-12.3 | 6.5-20.0 | |
| Directional resolution range (Å) | 4.4-6.7 | 6.2-9.4 | |
| Sphericity of 3DFSC | 0.95 | 0.87 | |
| Refinement | |||
| Initial model used (PDB code) | 3LZ0,3AFA,4Z2M,4IFS | ||
| Model resolution (Å) | 5.25 | 7.3 | |
| FSC threshold | 0.143 | 0.143 | |
| Model resolution range (Å) | 4.8-7.1 | 6.6-7.9 | |
| Map sharpening B factor (Å2) | 151.0 | 382.7 | |
| Model composition | |||
| Non-hydrogen atoms | 13861 | 15882 | |
| Protein residues | 1368 | 1589 | |
| Nucleotide | 144 | 158 | |
| B factors (Å2)* | |||
| Protein | 524 | 408 | |
| Nucleotide | 470 | 411 | |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.006 | 0.005 | |
| Bond angles (°) | 1.101 | 1.090 | |
| Validation | |||
| MolProbity score | 2.26 | 2.25 | |
| Clashscore | 20.32 | 21.65 | |
| Poor rotamers (%) | 0.00 | 0.23 | |
| Ramachandran plot | |||
| Favored (%) | 92.85 | 93.55 | |
| Allowed (%) | 7.15 | 6.32 | |
| Disallowed (%) | 0.00 | 0.13 | |