Table 2. Data collection and refinement statistics for cryo-EM Structures I-V.
| STRUCTURE | I | II | III | IV | V |
|---|---|---|---|---|---|
| PDB ID EMD code |
6OFX 20048 |
6OG7 20052 |
6OGF 20056 |
6OGG 20057 |
6OGI 20058 |
| Data collection | |||||
| EM equipment | FEI Titan Krios | ||||
| Voltage (kV) | 300 | ||||
| Detector | K2 summit | ||||
| Pixel size (Å) | 1.33 | ||||
| Electron dose (e-/Å2) | 29.4 | ||||
| Defocus range (μm) | – 0.5 – 1.8 | ||||
| Reconstruction | |||||
| Software | Frealign v9.11 | ||||
| Number of particles in final map | 102,723 | 62,029 | 28,549 | 5,881 | 63,383 |
| Final resolution (Å) | 3.3 | 3.3 | 3.7 | 4.4 | 3.4 |
| Average sharpening B factor (Å2) | -30 | -26 | -17 | -4 | -30 |
| Structure Refinement | |||||
| Model Fitting | Chimera/Pymol | ||||
| Refinement | |||||
| Software | RSRef/Phenix | ||||
| Correlation Coefficient,cc_mask* | 0.83 | 0.84 | 0.84 | 0.76 | 0.82 |
| Real-space R-factor † | 0.25 | 0.23 | 0.22 | 0.25 | 0.25 |
| Validation (proteins) | |||||
| MolProbity Score ‡ | 2.22 | 2.34 | 2.42 | 2.26 | 2.24 |
| Clash score, all atoms ‡ | 17.4 | 17.4 | 16.5 | 15.1 | 16.3 |
| Poor rotamers (%) ‡ | 0.4 | 0.7 | 0.7 | 0.6 | 0.5 |
| Favored/allowed rotamers (%) ‡ | 99.6 | 99.3 | 99.3 | 99.4 | 99.5 |
| Ramachandran-plot statistics | |||||
| Outlier (%) ‡ | 0 | 0.6 | 0.8 | 0.0 | 0.4 |
| Favored (%) ‡ | 92.2 | 88.1 | 82.3 | 89.0 | 90.7 |
| R.m.s. deviations †,§ | |||||
| Bond length (Å) | 0.008 | 0.006 | 0.006 | 0.006 | 0.009 |
| Bond angle (°) | 1.064 | 0.892 | 0.922 | 0.848 | 1.113 |
| Validation (RNA) | |||||
| Good sugar puckers (%) ‡ | 99.7 | 99.8 | 99.8 | 99.8 | 99.8 |
| Good backbone conformation (%) ‡ | 82.9 | 84.6 | 85.0 | 85.0 | 82.0 |
*from Phenix.
†from RSRef.
§root-mean-square deviations.
# RNA backbone suites that fall into recognized rotamer conformations defined by MolProbity.