Table 1 Cryo-EM data collection, refinement and validation statistics
From: SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation
43S PIC–Nsp1 (EMD-11323) | Non-translating 80S–Nsp1 (EMD-11609) | ||||
|---|---|---|---|---|---|
Data collection and processing | |||||
Magnification | 81,000× (nominal) | ||||
Voltage (kV) | 300 | ||||
Electron exposure (e−/Å2) | 60 | ||||
Defocus range (μm) | 1–3 | ||||
Pixel size (Å) | 1.08 (super-resolution pixel at 0.54 Å per pixel) | ||||
Initial particle images (no.) | 2,078,577 | 2,078,577 | 2,078,577 | 1,358,638 | 1,358,638 |
Final particle images (no.) | 118,765 | 118,765 | 118,765 | 18,692 | 300,147 |
Map resolution (Å) | 2.8 | 2.8 | 2.8 | 4.1 | 2.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Refinement | |||||
Model resolution (Å) | 2.8 | 2.8 | 2.8 | – | – |
FSC threshold | 0.5 | 0.5 | 0.5 | – | – |
Map sharpening B factor (Å2) | −62.2 | −62.8 | −70 | – | – |
Model composition | |||||
Non-hydrogen atoms | 25,591 | 50,192 | 75,783 | – | – |
Protein residues | 1,944 | 2,970 | 4,914 | – | – |
RNA residues | 472 | 1,232 | 1,704 | – | – |
Ligands: Mg2+/ Zn2+ | 57/2 | 109/1 | 166/3 | – | – |
B factors (Å2) | |||||
Protein | 12/80/36 | 4/50/15 | 15/112/46 | – | – |
RNA | 7/117/28 | 3/89/25 | 12/175/52 | – | – |
Ligand | 9/91/19 | 4/38/9 | 13/100/31 | – | – |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.003 | 0.002 | 0.002 | – | – |
Bond angles (°) | 0.535 | 0.512 | 0.500 | – | – |
Validation | |||||
MolProbity score | 1.49 | 1.36 | 1.39 | – | – |
Clashscore | 3.96 | 4.02 | 4.34 | – | – |
Poor rotamers (%) | 1.49 | 1.48 | 1.39 | – | – |
Ramachandran plot | |||||
Favored (%) | 96.97 | 97.81 | 97.69 | – | – |
Allowed (%) | 3.02 | 2.19 | 2.31 | – | – |
Disallowed (%) | 0 | 0 | 0 | – | – |
