Table 2.
Cryo-EM data collection, refinement and validation statistics.
| spike-BAP Wuhan + H6 | spike hexaPro Omicron + H6 3Up |
spike hexaPro Omicron + H6
2Up1Down |
|
|---|---|---|---|
| data collection and processing | |||
| magnification | 81 000 | 120 000 | 120 000 |
| voltage (kV) | 300 | 200 | 200 |
| electron exposure (e−/Å2) | 50.1 | 40.5 | 40.5 |
| defocus range (μm) | 1.0–2.5 | 1.5–3.0 | 1.5–3.0 |
| pixel size (Å/pix) (super-resolution) | 1.072 | 1.2 | 1.2 |
| symmetry imposed | C1 | C1 | C1 |
| initial particle images (no.) | — | 568 299 | 568 299 |
| final particle images (no.) | — | 104 001 | 131 621 |
| map resolution (Å) | — | 3.8 | 4 |
| FSC threshold | — | 0.143 | 0.143 |
| map resolution range (Å) | — | ||
| refinement a | |||
| initial model used | — | 7QO7 | 7QO7 |
| model resolution (Å) | — | 3.9 | 4.0 |
| FSC threshold | — | 0.143 | 0.143 |
| model resolution range (Å) | — | 2.9–5.3 | 3.1–6.2 |
| map sharpening B factor (Å2) | — | −107 | −145 |
| model composition | — | ||
| non-hydrogen atoms | — | 29 170 | 28 223 |
| protein residues | — | 3674 | 3544 |
| B factors (Å2) | — | ||
| protein | — | 400 | 352 |
| r.m.s. deviations | — | ||
| bond lengths (Å) | — | 0.008 | 0.007 |
| bond angles (°) | — | 1.08 | 0.72 |
| validation | |||
| MolProbity score | — | 2.2 | 2.04 |
| clashscore | — | 19.2 | 13 |
| poor rotamers (%) | — | 0.4 | 0.2 |
| Ramachandran plot | — | ||
| favoured (%) | — | 93 | 94 |
| allowed (%) | — | 6.6 | 5.7 |
| disallowed (%) | — | 0.4 | 0.3 |
a
Nanobody excluded from refinement