Table 1 Cryo-EM data collection, refinement and validation statistics
TXNL1 + proteasome PDB 9BW4, EMD-44952 | TXNL1 + proteasome (local refinement) EMD-44949 | |
|---|---|---|
Data collection and processing | ||
Magnification | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e−/Å2) | 50 to 54 | 50 to 54 |
Defocus range (μm) | −0.8 to −2.2 | −0.8 to −2.2 |
Pixel size (Å) | 0.825 | 0.825 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 1,765,798 | 1,765,798 |
Final particle images (no.) | 103,163 | 103,163 |
Map resolution (Å) | 3.3 | 3.0 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.9 to 51.6 | 2.5 to 25.0 |
Refinement | ||
Initial model used (PDB code) | AlphaFold2, ModelAngelo | |
Model resolution (Å) | 3.8 | |
FSC threshold | 0.5 | |
Model resolution range (Å) | 3.8 to 82.8 | |
Map sharpening B factor (Å2) | −55.6 | |
Model composition | ||
Non-hydrogen atoms | 90,418 | |
Protein residues | 11,464 | |
Ligands | 1 Zn2+ | |
5 Mg2+ | ||
3 ATP | ||
3 ADP | ||
B factors (Å2) | ||
Protein | 80.37 | |
Ligand | 75.31 | |
R.m.s. deviations | ||
Bond lengths (Å) | 0.006 | |
Bond angles (°) | 1.033 | |
Validation | ||
MolProbity score | 2.33 | |
Clashscore | 17.92 | |
Poor rotamers (%) | 0.03 | |
Ramachandran plot | ||
Favored (%) | 88.86 | |
Allowed (%) | 11.06 | |
Disallowed (%) | 0.08 | |
