Table 3.
Cryo-EM data collection, refinement and validation statistics for LSU
| Dataset 1 (EMDB-16530) (PDB 8CAM) | Dataset 2 (EMDB-16613) (PDB 8CEU) | Dataset 3 (EMDB-16646) (PDB 8CGK) | Dataset 4 (EMDB-16641) (PDB 8CGD) | Dataset 5 (EMDB-16652) (PDB 8CGV) | |
|---|---|---|---|---|---|
| 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) | 1.86 | 1.83 | 1.64 | 1.98 | 1.65 |
| 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) | 1.9 | 1.8 | 1.6 | 2.0 | 1.7 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| CC (mask) | 0.76 | 0.85 | 0.80 | 0.84 | 0.77 |
| CC (volume) | 0.76 | 0.84 | 0.78 | 0.82 | 0.76 |
| Map sharpening B factor (Å2) | −26.4 | −18.0 | −32.0 | −22.0 | −27.0 |
| Model composition | |||||
| Nonhydrogen atoms | 86,648 | 92,830 | 88,150 | 94,181 | 87,899 |
| Protein residues | 2,767 | 3,028 | 2,792 | 3,059 | 2,819 |
| RNA residues | 2,724 | 2,872 | 2,738 | 2,867 | 2,743 |
| Waters | 6,113 | 6,830 | 7,101 | 8,357 | 6,570 |
| Magnesium (MG) | 246 | 220 | 260 | 254 | 219 |
| Potassium (K) | 72 | 81 | 81 | 85 | 83 |
| Antibiotics* | 6O1 | G34, CA7 (8) | 3QB, 6UQ | CLY, AM2 | MUL, P8F (2) |
| B factors (Å2) | |||||
| Protein | 52.68 | 48.60 | 36.22 | 50.57 | 43.14 |
| RNA | 57.51 | 44.15 | 41.64 | 45.61 | 40.17 |
| Ligand | 51.25 | 58.66 | 23.33 | 37.21 | 31.73 |
| Water | 41.80 | 38.02 | 30.76 | 42.29 | 36.51 |
| R.m.s. deviations | |||||
| Bond lengths (Å) | 0.009 | 0.008 | 0.008 | 0.008 | 0.008 |
| Bond angles (°) | 1.547 | 1.556 | 1.531 | 1.579 | 1.585 |
| Validation | |||||
| MolProbity score | 0.90 | 0.82 | 0.67 | 0.85 | 0.74 |
| Clashscore | 0.61 | 0.53 | 0.37 | 0.70 | 0.52 |
| Poor rotamers (%) | 0.27 | 0.65 | 0.26 | 0.36 | 0.35 |
| Ramachandran plot | |||||
| Favored (%) | 96.84 | 97.22 | 97.84 | 97.36 | 97.71 |
| Allowed (%) | 3.05 | 2.74 | 2.16 | 2.58 | 2.29 |
| Disallowed (%) | 0.11 | 0.03 | 0.00 | 0.07 | 0.00 |
| Ramachandran Z score | −1.28 | −1.11 | −0.57 | −0.73 | −0.49 |
a6O1 (evernimicin), G34 (retapamulin), CA7 (capreomycin), 3QB (lincomycin), 6UQ (avilamycin), CLY (clindamycin), AM2 (apramycin), MUL (tiamulin), P8F (pentacycline).