Extended Data Table 2. Cryo-EM data acquisition and structure determination.
| PDD1 (EMD-15285, PDB 8A9L) |
|
|---|---|
| Data acquisition | |
| Electron gun | CFEG |
| Detector | Falcon 4i |
| Energy filter slit (eV) | 10 |
| Magnification | 165,000 |
| Voltage (kV) | 300 |
| Electron dose (e–/Å2) | 40 |
| Defocus range (μm) | 0.6 to 1.4 |
| Pixel size (Å) | 0.727 |
| Map refinement | |
| Symmetry imposed | C1 |
| Initial particle images (no.) | 566649 |
| Final particle images (no.) | 68330 |
| Map resolution (Å) | 2.2 |
| FSC threshold | 0.143 |
| Helical twist (°) | 0.86 |
| Helical rise (Å) | 4.76 |
| Model refinement | |
| Model resolution (Å) | 2.2 |
| FSC threshold | 0.5 |
| Map sharpening B factor (Å2) | -35 |
| Model composition | |
| Non-hydrogen atoms | 2880 |
| Protein residues | 430 |
| Ligands | 0 |
| B factors (Å2) | |
| Protein | 44.5 |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.0063 |
| Bond angles (°) | 1.16 |
| Validation | |
| MolProbity score | 1.6 |
| Clashscore | 6.34 |
| Poor rotamers (%) | 0 |
| Ramachandran plot | |
| Favored (%) | 96.25 |
| Allowed (%) | 3.75 |
| Disallowed (%) | 0 |