Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural insights into MERS and SARS coronavirus membrane proteins
SARS-CoV apo (EMD-49950) (PDB 9NZ4) | SARS-CoV JNJ-9676 (EMD-49949) (PDB 9NZ3) | MERSmut-CoV apo (EMD-49951) (PDB 9NZ5) | |
|---|---|---|---|
Data collection and processing | |||
Magnification | 105,000 | 105,000 | 105,000 |
Voltage (kV) | 200 | 200 | 300 |
Electron exposure (electrons/Å2) | 40 | 40 | 51.96 |
Defocus range (μm) | −0.6 to −2.0 | −0.6 to −2.0 | −1.4 to −2.3 |
Pixel size (Å) | 0.910 | 0.910 | 0.837 |
Symmetry imposed | C1 | C1 | C1 |
Initial particle images (no.) | 1,589,789 | 1,294,716 | 2,739,392 |
Final particle images (no.) | 1,210,771 | 674,469 | 827,876 |
Map resolution (Å) FSC threshold | 3.23 0.143 | 3.07 0.143 | 3.15 0.143 |
Map resolution range (Å) | 2.8–5.5 | 2.7–4.4 | 2.2–4.5 |
Refinement | |||
Initial model used (PDB code) | 7VGS | 8W2E | 7VGS |
Model resolution (Å) FSC threshold | 3.23 0.143 | 3.07 0.143 | 3.15 0.143 |
Model resolution range (Å) | 3.1–3.5 | 3.0–3.4 | 3.0–3.3 |
Model composition Non-hydrogen atoms Protein residues Ligands | 9688 1246 0 | 9663 1234 2 | 9681 12480 |
B factors (Å2) (min/max/mean) Protein Ligand Water | 0.00/600.00/63.31 | 8.12/190.21/80.30 23.26/47.84/34.46 8.26/8.26/8.26 | 23.29/225.39/108.51 |
R.m.s. deviations Bond lengths (Å) Bond angles (°) | 0.011 (2) 1.075 (1) | 0.004 (0) 0.778 (5) | 0.004 (0) 0.844 (2) |
Validation MolProbity score Clashscore Poor rotamers (%) | 1.22 1.51 0.46 | 1.83 6.69 0.19 | 1.74 5.31 0.18 |
Ramachandran plot Favored (%) Allowed (%) Disallowed (%) | 95.30 4.21 0.49 | 92.64 7.12 0.25 | 92.80 7.12 0.08 |
