Table 2 Data collection, processing, model refinement and validation
DrOTOP1_C2.2 | DrOTOP1_C11 | DrOTOP_C2.36 | |
|---|---|---|---|
Data collection and processing | |||
Magnification | 105,000 | 29,000 | 190,000 |
Voltage (kV) | 300 | 200 | 200 |
Electron exposure (e–/Å2) | 49.90 | 50.37 | ~ 40–50 |
Defocus range (μm) | −0.7 to −1.5 | −0.8 to −1.8 | −0.8 to −1.8 |
Pixel size (Å) | 0.833 | 1.150 | 0.725 |
Initial particle images (no.) | 6,147,309 | 3,410,686 | 7,236,014 |
Symmetry imposed | C2 | C2 | C2 |
Final particle images (no.) | 155,580 | 164,766 | 290,491 |
Map resolution (Å) | 3.23 | 3.73 | 3.42 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Å2) | −150.6 | −102.2 | −104.9 |
Model | |||
Composition | |||
Peptide chains | 2 | 2 | 2 |
Protein residues | 782 | 708 | 734 |
Ligands | 14 | 8 | 12 |
R.m.s. deviations | |||
Bond lengths (Å) | 0.006 | 0.006 | 0.007 |
Bond angles (°) | 0.971 | 1.007 | 1.011 |
Validation | |||
MolProbity score | 0.56 | 0.76 | 0.85 |
Clashscore | 0.15 | 0.85 | 1.30 |
EMRinger score | 2.39 | 1.9 | 2.13 |
Poor rotamers (%) | 0.00 | 0.65 | 0.00 |
Ramachandran plot | |||
Favored (%) | 99.73 | 98.52 | 99.42 |
Allowed (%) | 0.27 | 1.48 | 0.58 |
Disallowed (%) | 0.00 | 0.00 | 0.00 |
Deposition ID | |||
EMDB | EMD-48227 | EMD-48234 | EMD-48235 |
PDB | 9MFF | 9MFL | 9MFM |
