Table 1.
Cryo-EM data collection, refinement, and validation statistics.
| VPS35L-VPS29-VPS26C (EMDB: 40885) (PDB: 8SYN) |
VPS35L(partial)-VPS29 (EMDB: 40884) (PDB: 8SYM) |
Composite Map (EMD: 40886) (PDB: 8SYO) |
|
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 105,000 | ||
| Voltage (kV) | 300 | ||
| Electron exposure (e−/Å−2) | 60 | ||
| Defocus range (μm) | −1.2 to −2.4 | ||
| Pixel size (Å) | 0.83 | ||
| Symmetry imposed | C1 | C1 | |
| Initial particle images (no.) | 1,221,095 | 426,624 | |
| Final particle images (no.) | 426,624 | 83,654 | |
| Map resolution (Å) | 2.9 | 3.2 | |
| FSC threshold | 0.143 | 0.143 | |
| Map pixel size (Å) | 1.0624 | 1.0624 | |
| Refinement | |||
| Initial model used (PDB code) | - | - | |
| Model composition | |||
| Nonhydrogen atoms | 10,070 | 4,487 | 10,070 |
| Protein residues | 1,259 | 560 | 1,259 |
| Ligands | 0 | 0 | 0 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.005 | 0.004 | 0.005 |
| Bond angles (°) | 0.550 | 0.454 | 0.550 |
| Validation | |||
| MolProbity score | 1.66 | 1.45 | 1.66 |
| Clashscore | 7.56 | 8.24 | 7.56 |
| Poor rotamers (%) | 0 | 0 | 0 |
| Ramachandran plot | |||
| Favored (%) | 96.4 | 98.0 | 96.4 |
| Allowed (%) | 3.6 | 2.0 | 3.6 |
| Disallowed (%) | 0 | 0 | 0 |
| Protein residues included in the model | VPS35L: 3–37, 110–139, 175–254, 268–924 VPS29: 3–186 VPS26C: 3–29, 38–56, 61–81, 86–127, 132–222, 225–297 |
VPS35L: 3–37, 580–602, 607–924 VPS29: 3–186 |
VPS35L: 3–37, 110–139, 175–254, 268–924 VPS29: 3–186 VPS26C: 3–29, 38–56, 61–81, 86–127, 132–222, 225–297 |