Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural basis for mTORC1 activation on the lysosomal membrane
mTORC1–RAG–Ragulator–4E-BP1 on membrane (EMD-47932) (PDB 9ED4) | ||||
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | 81,000 | 81,000 | 81,000 | 81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | ~30 | ~30 | ~30 | ~30 |
Defocus range (μm) | −0.9 to −2.0 | −0.9 to −2.0 | −0.9 to −2.0 | −0.9 to −2.0 |
Pixel size (Å) | 1.05 | 1.05 | 1.05 | 1.05 |
Symmetry imposed | C2 | C2 symmetry expanded, C1 | C2 symmetry expanded, C1 | C2 symmetry expanded, C1 |
Initial particle images (no.) | 54,935,004 (blob picking) | 54,935,004 (blob picking) | 54,935,004 (blob picking) | 54,935,004 (blob picking) |
Final particle images (no.) | 359,012 | 109,105 | 133,193 | 190,751 |
Map resolution (Å) | 3.23 overall (3.12/2.98 local refine) | 3.16 | 3.61 | 3.98 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | ~2.3 to ~38 ~2.3 to ~40.2 | ~2.3 to ~41.9 | ~2.2 to ~41.2 | ~3.37 to ~41.4 |
Refinement | ||||
Initial model used (PDB code) | 7UXH (mTOR, RAPTOR and RHEB are from AlphaFold) | 7UXH (mTOR and RHEB are from AlphaFold) | 7UXH (mTOR and RHEB are from AlphaFold) | |
Model resolution (Å) | 3.3 | 4.0 | 3.5 | 4.3 |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 |
Map sharpening B factor (Å2) | −84.9 | −91.9 | −74.9 | −121.4 |
Model composition | ||||
Non-hydrogen atoms | 80,794 | 22,106 | 22,420 | 11,246 |
Protein residues | 10,098 | 2,754 | 2,792 | 1,421 |
Ligands | 18 | 4 | 6 | 3 |
B factors (Å2) | ||||
Protein | 83.03 | 141.97 | 92.39 | 108.48 |
Ligand | 77.58 | 123.73 | 93.87 | 94.16 |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.004 | 0.004 | 0.004 | 0.005 |
Bond angles (°) | 0.729 | 0.682 | 0.660 | 1.170 |
Validation | ||||
MolProbity score | 1.80 | 1.83 | 1.67 | 1.92 |
Clashscore | 7.99 | 9.61 | 7.22 | 8.94 |
Poor rotamers (%) | 0.00 | 0.00 | 0.00 | 0.00 |
Ramachandran plot | ||||
Favoured (%) | 94.75 | 95.35 | 96.03 | 93.05 |
Allowed (%) | 5.13 | 4.61 | 3.97 | 6.74 |
Disallowed (%) | 0.12 | 0.04 | 0.00 | 0.22 |
