Extended Data Table 1.
Statistics of data collection, structural refinement and model validation
| Batches | Electron Microscope | Camera | Micrographs (Original micrographs) | Particles for 2D classification | Particles for 3D classification |
|---|---|---|---|---|---|
| 1 | F20 | US4000 | 381(966) | 76,323 | 19,253 |
| 2 | Titan Krios | Eagle | 3,184(4,701) | 154,785 | 133,455 |
| 3 | Titan Krios | K2 | 1,017(1,136) | 90,888 | 35,096 |
| 4 | Titan Krios | K2 | 1,497(1,579) | 200,292 | 100,956 |
| 5 | Titan Krios | K2 | 997(1,002) | 128,515 | 54,574 |
| 6 | Titan Krios | K2 | 1,114(1,114) | 139,309 | 54,257 |
| 7 | Titan Krios | K2 | 1,014(1,016) | 134,937 | 50,334 |
| 8 | Titan Krios | K2 | 833(852) | 184,222 | 143,707 |
| 9 | Titan Krios | K2 | 901(901) | 225,167 | 146,349 |
| 10 | Titan Krios | K2 | 1,019(1019) | 248,518 | 157,947 |
| Data Collection | |
| EM equipment | FEI Titan krios |
| Voltage (kV) | 300 |
| Detector | Gatan K2 |
| Particles | 191,848 |
| Pixel size (Å) | 1.32 |
| Defocus range (μm) | 1.0–2.0 |
| Electron dose (e−/Å2) | 50 (32 frames)/22 (frame 3–16) |
| Model composition | |
| Peptide chains | 54 |
| Protein residues | 13,982 |
| RNA chains | 3 |
| RNA bases | 3,446 |
| Refinement | |
| Resolution (Å) | 3.08 |
| Map sharpening B-factor (Å2) | −65 |
| R factor | 0.3040 |
| Fourier Shell Correlation | 0.7814 |
| Rms deviations | |
| Bonds (Å) | 0.0054 |
| Angels(°) | 0.9687 |
| Validation (proteins) | |
| Molprobity score | 2.43 (96th percentile) |
| Clashscore, all atoms | 3.44 (100th percentile) |
| Good rotamers (%) | 80.87 |
| Ramachandran plot | |
| Favored (%) | 88.14 |
| Outliers (%) | 3.46 |
| Validation (RNA) | |
| Correct sugar puckers (%) | 97.16 |
| Good backbone conformations (%) | 71.60 |