Table 1 Cryo-EM data collection, refinement and validation statistics
From: Lis1 relieves cytoplasmic dynein-1 autoinhibition by acting as a molecular wedge
DyneinE2488Q bound to Lis1 in Chi conformation. EMD-27810, PDB 8DZZ | DyneinE2488Q bound, to Lis1 in Chi, conformation, symmetry expansion, EMD-27811, PDB 8E00 | Dynein bound, to Lis1 in the presence of ATP | |
|---|---|---|---|
Data collection and processing | |||
Magnification | 38,000 | 38,000 | 36,000 |
Voltage (kV) | 300 | 300 | 200 |
Electron exposure (e–/Å2) | 58.3 | 58.3 | 51.0 |
Defocus range (μm) | 2–2.7 | 2–2.7 | 0.8–2.4 |
Pixel size (Å) | 1.31 | 1.31 | 1.16 |
Symmetry imposed | C2 | C1 | |
Initial particle images (no.) | 561,397 | 561,397 | |
Final particle images (no.) | 23,385 | 46,770 | |
Map resolution (Å) | 4.1 | 3.6 | |
FSC threshold | 0.143 | 0.143 | |
Map resolution range (Å) | 4.0–6.0 | 3.5–6.0 | |
Refinement | |||
Initial model used (PDB code) | |||
Model resolution (Å) | 4.4 | 3.9 | |
FSC threshold | 0.5 | 0.5 | |
Map sharpening B factor (Å2) | 106.5 | 90.5 | |
Model composition | |||
Non-hydrogen atoms | 49,596 | 24,794 | |
Protein residues | 6,110 | 3,055 | |
Ligands | 8 | 4 | |
B factors (Å2) | |||
Protein | 154.6 | 94.0 | |
Ligand | 132.4 | 77.6 | |
R.m.s. deviations | |||
Bond lengths (Å) | 0.005 | 0.005 | |
Bond angles (°) | 1.087 | 1.124 | |
Validation | |||
MolProbity score | 1.11 | 0.98 | |
Clashscore | 3.00 | 2.10 | |
Poor rotamers (%) | 0.25 | 0.47 | |
Ramachandran plot | |||
Favored (%) | 98.39 | 98.21 | |
Allowed (%) | 1.57 | 1.76 | |
Disallowed (%) | 0.03 | 0.03 | |
