Table 2 The statistics of cryo-EM data collection, structure refinement, and validation for the apo-AsfvTop2 structure in three states, containing six conformers
From: A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase
apo-AsfvTop2 | ||||||
|---|---|---|---|---|---|---|
Data collection and processing | ||||||
Micrographs | 8900 | |||||
Magnification | 105,000 | |||||
Voltage (kV) | 300 | |||||
Electron exposure (e–/Å2) | 50 | |||||
Defocus range (μm) | −1.5 ~-2.5 | |||||
Pixel size (Ã…) | 0.83 | |||||
Symmetry imposed | C2 | |||||
Initial particle images (no.) | 3,260,785 | |||||
Conformer | Ia | Ib | IIa | IIb | IIIa | IIIb |
PDB/EMDB code | 8J87/EMD-36062 | 8J88/EMD-36063 | 8J89/EMD-36064 | 8J8A/EMD-36065 | 8J8B/EMD-36066 | 8J8C/EMD-36067 |
Final particle images (no.) | 79,500 | 75,839 | 567,069 | 393,995 | 341,283 | 180,474 |
Map resolution (Ã…) | 3.42 | 3.49 | 2.31 | 2.51 | 2.43 | 2.69 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 3.0–15.0 | 3.0–15.0 | 2.0–8.0 | 2.0–9.0 | 2.0–8.0 | 2.0–10.0 |
Refinement | ||||||
Initial model used (PDB code) | 1ZVU47 | Ia(8J87) | Robetta prediction81 | IIa(8J89) | IIa(8J89) | IIIa(8J8B) |
Model resolution (Ã…) | 3.42 | 3.49 | 2.31 | 2.51 | 2.43 | 2.69 |
Model resolution range (Å) | 3.0–15.0 | 3.0–15.0 | 2.0–8.0 | 2.0–9.0 | 2.0–8.0 | 2.0–10.0 |
Map sharpening B factor (Å2) | −96.5 | −111.5 | −80.8 | −86.7 | −79.7 | −79.7 |
Model composition | ||||||
Protein residues | 954 | 954 | 1502 | 1502 | 1518 | 1434 |
Non-hydrogen atoms | 7846 | 7846 | 12,222 | 12,222 | 12,330 | 11,650 |
Ligand | 0 | 0 | 0 | 0 | 0 | 0 |
B factors (Ã…2) | ||||||
Protein | 157.69 | 194.85 | 96.39 | 110.18 | 109.82 | 104.39 |
R.m.s. deviations | ||||||
Bond lengths (Ã…) | 0.002 | 0.002 | 0.002 | 0.003 | 0.002 | 0.002 |
Bond angles (°) | 0.562 | 0.562 | 0.457 | 0.498 | 0.432 | 0.432 |
Validation | ||||||
MolProbity score | 1.66 | 1.64 | 1.56 | 1.41 | 1.50 | 1.54 |
Clash score | 7.20 | 5.61 | 5.77 | 7.45 | 5.43 | 4.89 |
Poor rotamers (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Ramachandran plot (%) | ||||||
Favored | 96.11 | 95.16 | 96.39 | 97.99 | 96.49 | 95.91 |
Allowed | 3.89 | 4.84 | 3.61 | 2.01 | 3.51 | 4.09 |
Disallowed | 0.0 | 0.0 | 0.00 | 0.00 | 0.00 | 0.00 |
