Extended Data Table 1.
Refinement statistics for all structures
| Structure I | Structure II | Structure III | Structure I-nc | Structure II- nc |
Structure III- nc |
|
|---|---|---|---|---|---|---|
| PDB code | 5UYK | 5UYL | 5UYM | 5UYN | 5UYP | 5UYQ |
| EMDB code | 8615 | 8616 | 8617 | 8618 | 8619 | 8620 |
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| Data collection | ||||||
| EM equipment | FEI Titan Krios | FEI Titan Krios | FEI Titan Krios | FEI Titan Krios | FEI Titan Krios | FEI Titan Krios |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
| Detector | K2 summit | K2 summit | K2 summit | K2 summit | K2 summit | K2 summit |
| Pixel size (Å) | 1.64 | 1.64 | 1.64 | 1.64 | 1.64 | 1.64 |
| Electron dose (e−/Å2) | 50 | 50 | 50 | 30 | 30 | 30 |
| Defocus range (µm) | 0.4 – 5.0 | 0.4 – 5.0 | 0.4 – 5.0 | 0.5 – 5.0 | 0.5 – 5.0 | 0.5 – 5.0 |
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|
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| Reconstruction | ||||||
| Software | Frealign v9.10–9.11 | Frealign v9.10–9.11 | Frealign v9.10–9.11 | Frealign v9.10–9.11 | Frealign v9.10–9.11 | Frealign v9.10–9.11 |
| Number of particles in final map | 6,726 | 10,431 | 153,597 | 4,629 | 6,910 | 5,758 |
| Final resolution (Å) | 3.9 | 3.6 | 3.2 | 4 | 3.9 | 3.8 |
| Map-sharpening B factor (Å2) | −36 | −50 | −100 | 0 | −25 | −25 |
| Model fitting | ||||||
| Software | Chimera & Pymol | Chimera & Pymol | Chimera & Pymol | Chimera & Pymol | Chimera & Pymol | Chimera & Pymol |
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| Model composition | ||||||
| Non-hydrogen atoms | 154,413 | 153,755 | 154,140 | 153,718 | 153,781 | 153,760 |
| Protein residues | 6,563 | 6,476 | 6,476 | 6,474 | 6,476 | 6,476 |
| RNA bases | 4,812 | 4,810 | 4,810 | 4,809 | 4,811 | 4,810 |
| Ligands (Zn2+/Mg2+) | 0, 0 | 0, 0 | 2, 383 | 0, 0 | 0, 0 | 0, 1 |
| Ligands/Modifications (GDPCP, fMet, Phe, Lys) | 1 (GDPCP) | 3 (GDPCP, fMet, Phe) | 3 (GDPCP, fMet, Phe) | 1 (GDPCP) | 3 (GDPCP, fMet, Lys) | 3 (GDPCP, fMet, Lys) |
| Refinement | ||||||
| Software | RSRef & Phenix | RSRef & Phenix | RSRef & Phenix | RSRef & Phenix | RSRef & Phenix | RSRef & Phenix |
| Correlation Coefficient* | 0.84 | 0.84 | 0.88 | 0.79 | 0.80 | 0.79 |
| Real space R-factor† | 0.19 | 0.19 | 0.20 | 0.20 | 0.20 | 0.20 |
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| Validation (proteins) | ||||||
| Molprobity Score‡ | 2.22 | 2.31 | 2.31 | 2.4 | 2.5 | 2.4 |
| Clash score, all atoms‡ | 12.0 | 13.1 | 13.0 | 13.6 | 13.3 | 14.5 |
| Poor rotamers (%)‡ | 0.9 | 1.1 | 1.2 | 1.1 | 1.6 | 1.3 |
| Favored rotamers (%)‡ | 94.9 | 93.8 | 94.6 | 93.6 | 92.8 | 92.9 |
| Ramachandran-plot statistics | ||||||
| Outlier (%)‡ | 1.7 | 2.2 | 2.0 | 2.8 | 3.1 | 2.7 |
| Favored (%)‡ | 86.4 | 85.6 | 86.5 | 83.5 | 82.6 | 84.5 |
| R.m.s. deviations†,§ | ||||||
| Bond length (Å) | 0.007 | 0.008 | 0.006 | 0.005 | 0.005 | 0.005 |
| Bond angle (°) | 0.9 | 0.9 | 0.9 | 0.9 | 0.9 | 0.9 |
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| Validation (RNA) | ||||||
| Good sugar puckers (%)‡ | 99.6 | 99.5 | 99.5 | 99.6 | 99.6 | 99.4 |
| Good backbone conformation (%)‡ | 88.4 | 88.2 | 88.4 | 88.4 | 88.3 | 87.1 |