Extended Data Table 1. Cryo-EM statistics for map and model refinement.
| Pre-Fusion pH8 (EMDB-10696) (PDB 6Y5G) | Pre-Fusion pH5 (EMDB-10697) (PDB 6Y5H) | Dilated Form 1 (EMDB-10698) (PDB 6Y5I) | Dilated Form 2 (EMDB-10699) (PDB 6Y5J) | Full Extended HA2 (EMDB-10700) (PDB 6Y5K) | Subtracted Extended HA2 (EMDB-10701) (PDB 6Y5L) | Post Fusion (EMDB-10702) | |
|---|---|---|---|---|---|---|---|
| State Number | - | I | II | III | IV | IV | V |
| Timepoint | - | 20 s | 10 s | 20 s | 20 s | 20 s | 30 min + 2-ME |
| Data collection and processing | |||||||
| Magnification | 75 000 | 75 000 | 75 000 | 75 000 | 75 000 | 75 000 | 75 000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 33.9 | 33.9 | 33.9 | 33.9 | 33.9 | 33.9 | 33.9 |
| Defocus range (μm) | 1.5-3 | 1.5-3 | 1.5-3 | 1.5-3 | 1.5-3 | 1.5-3 | 1.5-3 |
| Pixel size (Å) | 1.09 | 1.09 | 1.09 | 1.09 | 1.09 | 1.09 | 1.09 |
| Symmetry imposed | C3 | C3 | Cl | Cl | C3 | C3 | C3 |
| Initial particle images (no.) | 643 k | 1.39 M | 1.53 M | 1.39 M | 1.39 M | 1.39 M | 2.24 M |
| Final particle images (no.) | 200 k | 157 k | 72 k | 124 k | 189 k | 546 k | 62 k |
| Map resolution (Å) | 3.0 | 3.0 | 5.5 | 5.6 | 4.2 | 3.6 | 9.9 |
| FSC threshold 0.143 | |||||||
| Refinement Software | CryoSPARC | CryoSPARC | CryoSPARC | CryoSPARC | CryoSPARC | CryoSPARC | RELION |
| Map resolution range (Å) | 2.6-3.4 | 2.6-3.4 | 5-9 | 5-9 | 3-5 | 3-7 | - |
| Refinement | |||||||
| Initial model used (PDB code) | 2YPG | 2YPG | 2YPG | 2YPG | 2YPG&1QU1 | 2YPG&1QU1 | - |
| Map sharpening B factor (Å2) | -172 | -170 | -283 | -322 | -170 | -225 | - |
| Model composition | |||||||
| Non-hydrogen atoms | 12036 | 11994 | 11928 | 9609 | 10617 | 3855 | - |
| Protein residues | 1470 | 1470 | 1470 | 1185 | 1335 | 477 | |
| R.m.s. deviations | |||||||
| Bond lengths (Å) | 0.005 | 0.004 | 0.004 | 0.005 | 0.005 | 0.004 | - |
| Bond angles (°) | 0.553 | 0.959 | 0.987 | 1.000 | 1.049 | 0.999 | |
| Validation | |||||||
| MolProbity score | 1.48 | 1.35 | 1.54 | 1.82 | 1.65 | 1.78 | - |
| Clashscore | 3.69 | 2.81 | 4.31 | 10.88 | 10.23 | 5.46 | - |
| Poor rotamers (%) | 0.94 | 0.70 | 0.47 | 0.94 | 0 | 0 | - |
| Ramachandran plot | |||||||
| Favored (%) | 95.4 | 95.9 | 95.3 | 96.2 | 97.35 | 92.16 | - |
| Allowed (%) | 4.6 | 4.1 | 4.7 | 3.8 | 2.65 | 7.84 | - |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 | - |