Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
ULK1C core (2:1:1) stoichiometry | ULK1C:PI3KC3- C1 supercomplex | ULK1C core (2:2:2) stoichiometry in PI3KC3-C1 mixture | ULK1C core (2:2:2) stoichiometry ATG13450–517 mutant | |
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | ×81,000 | ×81,000 | ×81,000 | ×36,000 |
Voltage (kV) | 300 | 300 | 300 | 200 |
Electron exposure (e− per Å2) | 50 | 50 | 50 | 50 |
Defocus range (μm) | −0.8 to −2.0 | −0.8 to −2.0 | −0.8 to −2.0 | −0.8 to −2.0 |
Pixel size (Å) | 1.05 | 1.05 | 1.05 | 1.115 |
Symmetry imposed | C1 | C1 | C1 | C1 |
Images | 8,468 | 589 (0° tilt) 6,973 (20° tilt) 3,740 (30° tilt) | 5,383 | 2,286 |
Initial particle images (no.) | 2,156,516 | 4,473,551 | 502,985 | 968,884 |
Final particle images (no.) | 267,719 | 21,937 | 97,987 | 149,409 |
Map resolution, global (Å) | 4.2 | 8.03 | 5.28 | 4.46 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.48–63.83 | 7.15–23.07 | 4.96–81.03 | 3.77–70.64 |
Refinement | ||||
Initial model used (PDB code) | AlphaFold2 model | AlphaFold2 model | ||
Model resolution (Å) | 3.7 | 8.7 | 6.8 | 6.5 |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 |
Model resolution range (Å) | 3.48–22.49 | 7.15–16.90 | 4.98–16.47 | 3.78–11.37 |
Map sharpening B factor (A2) | 143.2 | 752.0 | 431.6 | 155.4 |
Model composition | ||||
Nonhydrogen atoms | 10,243 | 11,172 | 7,438 | 5,773 |
Protein residues | 1,276 | 2,254 | 1,498 | 1,163 |
Ligands | 0 | 0 | 0 | 0 |
B factors (Å2) | ||||
Protein | 126.43 | 1,099.03 | 319.79 | 208.69 |
Ligands | - | - | - | - |
Root-mean-square deviations | ||||
Bond lengths (Å) | 0.003 | 0.002 | 0.004 | 0.002 |
Bond angles (°) | 0.598 | 0.607 | 0.633 | 0.405 |
Validation | ||||
MolProbity score | 1.7 | 2.48 | 1.95 | 1.51 |
Clashscore | 9.52 | 30.51 | 8.07 | 4.44 |
Poor rotamers (%) | 1.5 | - | - | - |
Ramachandran plot | ||||
Favored (%) | 96.75 | 91.17 | 91.41 | 95.87 |
Allowed (%) | 3.17 | 8.83 | 8.59 | 4.13 |
Disallowed (%) | 0.008 | 0 | 0 | 0 |
