Table 1 Cryo-EM data collection, refinement, and validation statistics.
From: Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA
PolD–PCNA–DNA complex (EMDB-10401) (PDB 6TH8) | |
|---|---|
Data collection and processing | |
Magnification | 165,000 |
Voltage (kV) | 300 |
Electron exposure (e–/Å2) | 40 |
Defocus range (μm) | −0.5 to −3.5 |
Pixel size (Å) | 0.83 |
Symmetry imposed | C1 |
Initial particle images (no.) | 269,251 |
Final particle images (no.) | 147,511 |
Map resolution (Å) | 3.77 |
FSC threshold | 0.143 |
Map resolution range (Å) | 3 to 6 |
Refinement | |
Initial model used (PDB code) | 5IJL, 5IHE, 6T7X |
Model resolution (Å) | 3.77 |
FSC threshold | 0.143 |
Model resolution range (Å) | 3 to 6 |
Map sharpening B factor (Å2) | 145.192 |
Model composition | |
Non-hydrogen atoms | 19,398 |
Protein residues | 2347 |
Ligands | 5 |
B factors (Å2) | |
Protein | 81.31 |
Ligand | 131.54 |
R.m.s. deviations | |
Bond lengths (Å) | 0.012 |
Bond angles (°) | 1.258 |
Validation | |
MolProbity score | 2.58 |
Clashscore | 38.66 |
Poor rotamers (%) | 0.94 |
Ramachandran plot | |
Favored (%) | 91.21 |
Allowed (%) | 8.66 |
Disallowed (%) | 0.13 |
