Cryo-EM data collection and model refinement statistics.
| Data collection and processing | pH-7 dataset | pH-5 dataset | pH-3 dataset |
|---|---|---|---|
| Microscope | FEI Titan Krios | FEI Titan Krios | FEI Titan Krios |
| Magnification | 165,000 | 165,000 | 165,000 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | ∼50 | ∼50 | ∼50 |
| Defocus range (μm) | 2.0–3.8 | 2.0–3.8 | 2.0–3.8 |
| Pixel size (Å) | 0.82 | 0.82 | 0.83 |
| Symmetry imposed | C5 | C5 | C5 |
| Number of images | ∼5,300 | ∼7,000 | ∼6,400 |
| Particles picked | ∼700,000 | ∼1 million | ∼690,000 |
| Particles refined | 86,201 | 351,643 | 214,463 |
| Refinement | |||
| Initial model used | 4NPQ monomer | 4NPQ monomer | 4NPQ monomer |
| Resolution (Å) | 4.1 | 3.4 | 3.6 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map sharpening B-factor | −278 | −223 | −225 |
| Model composition | |||
| Non-hydrogen protein atoms | 10,175 | 11,555 | 11,630 |
| Protein residues | 1,440 | 1,540 | 1,535 |
| Ligands | 0 | 0 | 0 |
| B-factor (Å2) | 57 | 20 | 34 |
| Root mean-squared deviation | |||
| Bond Lengths (Å) | 0.006 | 0.005 | 0.006 |
| Bond angles (°) | 0.616 | 0.599 | 0.664 |
| Validation | |||
| MolProbity score | 1.87 | 1.93 | 1.77 |
| Clashscore | 10.73 | 9.66 | 6.12 |
| Poor rotamers (%) | 0 | 0 | 0 |
| Ramachandran plot | |||
| Favored (%) | 95.4 | 93.7 | 93.4 |
| Allowed (%) | 4.6 | 6.3 | 6.6 |
| Outliers (%) | 0 | 0 | 0 |