Cryo-EM data collection, refinement, and validation statistics
| . | Rigor-HA (8EFI) . | ADP-HA (8EFH) . | Rigor-SP (8EFE) . | ADP-SP (8EFD) . |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 81,000× | 81,000× | 81,000× | 81,000× |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 53.62 | 53.62 | 53.62 | 53.62 |
| Defocus range (μm) | −1.0 ∼ −3.0 | −1.0 ∼ −3.0 | −1.0 ∼ −3.0 | −1.0 ∼ −3.0 |
| Pixel size (Å) | 1.078 | 1.078 | 1.078 | 1.078 |
| Symmetry imposed | Helical symmetry | Helical symmetry | None | None |
| Initial segment images (no.) | 1,045,903 | 628,787 | 176,178 | 131,194 |
| Final segment images (no.) | 176,178 | 131,194 | 88,048 | 68,358 |
| Map resolution (Å) FSC threshold | 3.4 0.143 | 3.3 0.143 | 3.8 0.143 | 3.8 0.143 |
| Map resolution range (Å) | 3.3–7.3 | 3.2–10.49 | N/A | N/A |
| Refinement | ||||
| Initial model used (PDB ID) | 6X5Z | 6X5Z | Rigor-HA | Rigor-HA |
| Model resolution (Å) FSC threshold | 3.5 0.5 | 3.5 0.5 | 4.4 0.5 | 4.1 0.5 |
| Model resolution range (Å) | 3.1–3.5 | 3.0–3.4 | 3.6–4.4 | 3.4–4.1 |
| Map sharpening B factor (Å2) | −71.49 | −52.13 | −83.37 | −72.94 |
| Model composition Non-hydrogen atoms Protein residues Ligands | 23,281 2,929 5 | 23,254 2,921 6 | 7,107 886 0 | 7,135 886 1 |
| B factors (Å2) Protein Ligand | 112.33 69.31 | 85.14 54.89 | 203.27 N/A | 218.65 151.65 |
| R.M.S. deviations Bond lengths (Å) Bond angles (°) | 0.003 0.575 | 0.002 0.544 | 0.002 0.492 | 0.002 0.515 |
| Validation MolProbity score Clashscore Poor rotamers (%) | 1.84 7.28 0.20 | 2.29 6.93 0.20 | 1.70 8.25 0.13 | 1.70 8.23 0.52 |
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) | 97.04 2.96 0.00 | 96.45 3.55 0.00 | 96.23 3.77 0.0 | 96.23 3.77 0.0 |
| . | Rigor-HA (8EFI) . | ADP-HA (8EFH) . | Rigor-SP (8EFE) . | ADP-SP (8EFD) . |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 81,000× | 81,000× | 81,000× | 81,000× |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 53.62 | 53.62 | 53.62 | 53.62 |
| Defocus range (μm) | −1.0 ∼ −3.0 | −1.0 ∼ −3.0 | −1.0 ∼ −3.0 | −1.0 ∼ −3.0 |
| Pixel size (Å) | 1.078 | 1.078 | 1.078 | 1.078 |
| Symmetry imposed | Helical symmetry | Helical symmetry | None | None |
| Initial segment images (no.) | 1,045,903 | 628,787 | 176,178 | 131,194 |
| Final segment images (no.) | 176,178 | 131,194 | 88,048 | 68,358 |
| Map resolution (Å) FSC threshold | 3.4 0.143 | 3.3 0.143 | 3.8 0.143 | 3.8 0.143 |
| Map resolution range (Å) | 3.3–7.3 | 3.2–10.49 | N/A | N/A |
| Refinement | ||||
| Initial model used (PDB ID) | 6X5Z | 6X5Z | Rigor-HA | Rigor-HA |
| Model resolution (Å) FSC threshold | 3.5 0.5 | 3.5 0.5 | 4.4 0.5 | 4.1 0.5 |
| Model resolution range (Å) | 3.1–3.5 | 3.0–3.4 | 3.6–4.4 | 3.4–4.1 |
| Map sharpening B factor (Å2) | −71.49 | −52.13 | −83.37 | −72.94 |
| Model composition Non-hydrogen atoms Protein residues Ligands | 23,281 2,929 5 | 23,254 2,921 6 | 7,107 886 0 | 7,135 886 1 |
| B factors (Å2) Protein Ligand | 112.33 69.31 | 85.14 54.89 | 203.27 N/A | 218.65 151.65 |
| R.M.S. deviations Bond lengths (Å) Bond angles (°) | 0.003 0.575 | 0.002 0.544 | 0.002 0.492 | 0.002 0.515 |
| Validation MolProbity score Clashscore Poor rotamers (%) | 1.84 7.28 0.20 | 2.29 6.93 0.20 | 1.70 8.25 0.13 | 1.70 8.23 0.52 |
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) | 97.04 2.96 0.00 | 96.45 3.55 0.00 | 96.23 3.77 0.0 | 96.23 3.77 0.0 |
Compilation of the relevant statistics for the cryo-EM reconstructions and subsequent atomic models.