Table 2.
Cryo-EM data collection, refinement and validation statistics for SSU body
| Dataset 1 (EMDB-16526) (PDB 8CAI) | Dataset 2 (EMDB-16612) (PDB 8CEP) | Dataset 3 (EMDB-16645) (PDB 8CGJ) | Dataset 4 (EMDB-16650) (PDB 8CGR) | Dataset 5 (EMDB-16651) (PDB 8CGU) | |
|---|---|---|---|---|---|
| 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) | 2.08 | 2.04 | 1.79 | 2.12 | 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 | 2.0 | 1.8 | 2.1 | 1.9 |
| FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
| CC (mask) | 0.81 | 0.85 | 0.83 | 0.88 | 0.81 |
| CC (volume) | 0.80 | 0.84 | 0.81 | 0.87 | 0.81 |
| Map sharpening B factor (Å2) | -32.2 | −24.5 | −53.9 | −5.1 | −36.6 |
| Model composition | |||||
| Nonhydrogen atoms | 37,814 | 35,490 | 38,708 | 35,552 | 35,196 |
| Protein residues | 1,552 | 1,279 | 1,523 | 1,272 | 1,266 |
| RNA residues | 1,114 | 1,077 | 1,161 | 1,090 | 1,071 |
| Waters | 1,416 | 1,933 | 1,616 | 1,928 | 1,869 |
| Magnesium (MG) | 55 | 54 | 63 | 57 | 58 |
| Potassium (K) | 29 | 25 | 25 | 28 | 24 |
| Antibiotics* | SCM, HY0 (3), 5I0 | KSG, CA7 (5) | TAC, 5I0 | AM2 (3) | LLL (4) |
| B factors (Å2) | |||||
| Protein | 82.43 | 53.52 | 59.68 | 55.00 | 60.73 |
| RNA | 54.40 | 40.44 | 45.74 | 48.01 | 48.21 |
| Ligand | 55.57 | 66.05 | 30.78 | 54.19 | 52.66 |
| Water | 49.17 | 39.57 | 32.33 | 42.61 | 46.19 |
| R.m.s. deviations | |||||
| Bond lengths (Å) | 0.008 | 0.008 | 0.008 | 0.007 | 0.008 |
| Bond angles (°) | 1.496 | 1.536 | 1.515 | 1.585 | 1.581 |
| Validation | |||||
| MolProbity score | 0.95 | 0.72 | 0.87 | 0.87 | 0.71 |
| Clashscore | 0.59 | 0.43 | 0.37 | 0.93 | 0.38 |
| Poor rotamers (%) | 0.86 | 0.66 | 0.40 | 0.10 | 0.38 |
| Ramachandran plot | |||||
| Favored (%) | 96.22 | 97.68 | 96.41 | 97.58 | 97.65 |
| Allowed (%) | 3.71 | 2.32 | 3.46 | 2.42 | 2.35 |
| Disallowed (%) | 0.07 | 0.00 | 0.14 | 0.00 | 0.00 |
| Ramachandran Z score | −1.66 | −0.88 | −1.33 | −0.51 | −0.61 |
aSCM (spectinomycin), HY0 (hygromycin B), 5I0 (streptomycin), KSG (kasugamycin), CA7 (capreomycin), TAC (tetracycline), AM2 (apramycin), LLL (gentamicin).