Table 1 Cryo-EM data collection and model statistics
From: Structural basis for Retriever-SNX17 assembly and endosomal sorting
| Â | 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 (Ã…) | 0.83 | |||
Symmetry imposed | C1 | |||
Initial particle images (no.) | 1,009,886 | |||
Final particle images (no.) | 227,973 | |||
Map resolution (Ã…) | 3.4 | 3.35 | 3.75 | Â |
FSC threshold | 0.143 | |||
Refinement | ||||
Initial model used | Â | AlphaFold Multimer model (ma-swt4h) | ||
Model composition | ||||
Nonhydrogen atoms | Â | 8601 | ||
Protein residues | Â | 1079 | ||
Ligand | Â | 0 | ||
R.m.s. deviations | ||||
Bond lengths (Ã…) | Â | 0.005 | ||
Bond angles (°) |  | 1.026 | ||
Validation | Â | |||
MolProbity score | Â | 1.93 | ||
Clashscore | Â | 13.06 | ||
Poor rotamers (%) | Â | 0.21 | ||
Ramachandran plot | ||||
Favored (%) | Â | 95.65 | ||
Allowed (%) | Â | 4.35 | ||
Disallowed (%) | Â | 0.00 | ||
Protein residues included in the model | Â | 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 | ||
