Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structure and interactions of the endogenous human Commander complex
Native Commander complex (EMDB-17342) | Crosslinked Commander complex, focused map 1 (EMDB-17339), (PDB 8P0V) | Crosslinked Commander complex, focused map 2 (EMDB-17341), (PDB 8P0X) | ||
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | 165,000 | 105,000 | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e−/Å2) | 42.8 | 59.0/56.0 | 59.0/56.0 | 59.0/56.0 |
Defocus range (μm) | 1.5–3.0 | 0.4–2.2 | 0.4–2.2 | 0.4–2.2 |
Pixel size (Å) | 0.820 | 0.846/0.862 | 0.846/0.862 | 0.846/0.862 |
Symmetry imposed | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 137,000 | 5,372,000 | 667,000 | 667,000 |
Final particle images (no.) | 90,000 | 667,000 | 125,000 | 13,000 |
Map resolution (Å) | 3.3 | 2.9 | 6.5 | 7.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.3–44.2 | 2.9-40.0 | 6.5-40.0 | 7.5–40.0 |
Refinement | ||||
Model resolution (Å) | 3.03 | 7.94 | 8.14 | |
FSC threshold | 0.5 | 0.5 | 0.5 | |
Model resolution range (Å) | 3.03–40.0 | 7.94–40.0 | 0.814–40.0 | |
Map sharpening B factor (Å2) | −77 | −546 | −511 | |
Model composition | ||||
Nonhydrogen atoms | 17,518 | 9,073 | 1,850 | |
Protein residues | 2,208 | 1,802 | 1,850 | |
Ligands | 0 | 0 | 0 | |
B factors (Å2) | ||||
Protein | 32.14 | 185.77 | 378.41 | |
Ligand | ||||
R.m.s. deviations | ||||
Bond lengths (Å) | 0.004 | 0.006 | 0.009 | |
Bond angles (°) | 0.644 | 1.199 | 1.409 | |
Validation | ||||
MolProbity score | 0.97 | 1.48 | 1.79 | |
Clashscore | 1.42 | 3.50 | 9.06 | |
Poor rotamers (%) | 0.41 | 0 | 0 | |
Ramachandran plot | ||||
Favored (%) | 97.57 | 95.07 | 95.64 | |
Allowed (%) | 2.39 | 4.54 | 4.25 | |
Disallowed (%) | 0 | 0.39 | 0 |
