Table 1.
Cryo-EM data collection and model statistics.
| VPS35L-VPS29-VPS26C-SNX17 (EMD-43873) | VPS35L (partial)-VPS26C-SNX17 (EMD-43870) | VPS35L (partial)-VPS29 (EMD-43871) | Composite map (EMD-43872) (PDB 9AU7) | |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 105,000 | |||
| Voltage (kV) | 300 | |||
| Electron exposure (e–/Å2) | 64 | |||
| Defocus range (μm) | −0.9 to −2.4 | |||
| Pixel size (Å) | 0.83 | |||
| Symmetry imposed | C1 | |||
| Initial particle images (no.) | 1,009,886 | |||
| Final particle images (no.) | 227,973 | |||
| Map resolution (Å) | 3.4 | 3.35 | 3.75 | |
| FSC threshold | 0.143 | |||
| Refinement | ||||
| Initial model used | AlphaFold Multimer model (ma-swt4h) | |||
| Model composition | ||||
| Nonhydrogen atoms | 8601 | |||
| Protein residues | 1079 | |||
| Ligand | 0 | |||
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.005 | |||
| Bond angles (°) | 1.026 | |||
| Validation | ||||
| MolProbity score | 1.93 | |||
| Clashscore | 13.06 | |||
| Poor rotamers (%) | 0.21 | |||
| Ramachandran plot | ||||
| Favored (%) | 95.65 | |||
| Allowed (%) | 4.35 | |||
| Disallowed (%) | 0.00 | |||
| Protein residues included in the model | VPS35L:115-131, 180-253, 264-349, 352-738, 742-755, 768-786 VPS29: 3-186 VPS26C: 1-53, 63-146, 150-297 SNX17: 458-470 |
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