Table 1.
Cryo-EM data collection, refinement and validation statistics for SSU head
| Dataset 1 (EMDB-16520) (PDB 8CA7) | Dataset 2 (EMDB-16536) (PDB 8CAZ) | Dataset 3 (EMDB-16615) (PDB 8CF1) | Dataset 4 (EMDB-16620) (PDB 8CF8) | Dataset 5 (EMDB-16644) (PDB 8CGI) | |
|---|---|---|---|---|---|
| Data collection and processing | |||||
| Magnification | ×165,000 | ×270,000 | ×270,000 | ×270,000 | ×105,000 |
| Acceleration voltage (kV) | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 11 | 6 | 6 | 6 | 25 |
| Defocus range (μm) | −0.4 to −1.6 | −0.4 to −1.0 | −0.4 to −1.0 | −0.4 to −1.0 | −0.4 to −1.6 |
| Pixel size (Å) | 0.53 | 0.45 | 0.45 | 0.45 | 0.51 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 754,663 | 219,953 | 757,044 | 464,723 | 2,146,827 |
| Final particle images (no.) | 514,855 | 179,724 | 419,159 | 275,137 | 1,301,160 |
| Map resolution (Å) | 2.06 | 2.11 | 1.82 | 2.20 | 1.89 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | |||||
| Initial model used (PDB code) | 7K00 | 7K00 | 7K00 | 7K00 | 7K00 |
| Model resolution (masked, Å) | 2.1 | 2.1 | 1.8 | 2.2 | 1.9 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| CC (mask) | 0.75 | 0.86 | 0.85 | 0.90 | 0.82 |
| CC (volume) | 0.74 | 0.85 | 0.83 | 0.89 | 0.81 |
| Map sharpening B factor (Å2) | −33.3 | −26.7 | −49.3 | −15.4 | −39.2 |
| Model composition | |||||
| Nonhydrogen atoms | 18,093 | 19,193 | 18,957 | 19,324 | 17,553 |
| Protein residues | 848 | 1,095 | 988 | 1,102 | 841 |
| RNA residues | 502 | 460 | 485 | 460 | 460 |
| Waters | 543 | 618 | 677 | 681 | 948 |
| Magnesium (MG) | 26 | 29 | 31 | 32 | 32 |
| Potassium (K) | 14 | 13 | 12 | 12 | 10 |
| Antibiotics* | SCM, U3B | – | TAC | YQM | P8F |
| B factors (Å2) | |||||
| Protein | 61.72 | 67.40 | 53.15 | 74.43 | 56.72 |
| RNA | 59.78 | 46.08 | 43.19 | 46.74 | 50.94 |
| Ligand | 37.73 | 32.92 | 27.78 | 39.57 | 39.21 |
| Water | 38.93 | 35.62 | 29.73 | 37.05 | 41.92 |
| R.m.s. deviations | |||||
| Bond lengths (Å) | 0.008 | 0.008 | 0.008 | 0.008 | 0.008 |
| Bond angles (°) | 1.520 | 1.521 | 1.501 | 1.542 | 1.577 |
| Validation | |||||
| MolProbity score | 0.89 | 0.89 | 0.90 | 1.04 | 0.78 |
| Clashscore | 0.60 | 0.52 | 0.76 | 0.76 | 0.63 |
| Poor rotamers (%) | 0.71 | 0.55 | 0.49 | 0.98 | 0.71 |
| Ramachandran plot | |||||
| Favored (%) | 96.84 | 96.63 | 97.08 | 95.76 | 97.69 |
| Allowed (%) | 3.03 | 3.27 | 2.81 | 4.06 | 2.19 |
| Disallowed (%) | 0.12 | 0.09 | 0.10 | 0.18 | 0.12 |
| Ramachandran Z score | −1.46 | −1.41 | −0.76 | −1.40 | −0.30 |
aSCM (spectinomycin), U3B (omadacycline), TAC (tetracycline), YQM (eravacycline), P8F (pentacycline)