Table 1 Cryo-EM data collection, refinement and validation statistics
From: DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp
Closed state (EMDB-25121, PDB 7SGZ) | Open state (EMDB-25122, PDB 7SH2) | |
|---|---|---|
Data collection and processing | ||
Magnification | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e−/Å2) | 65 | 65 |
Defocus range (μm) | 1.1–1.9 | 1.1–1.9 |
Pixel size (Å) | 0.828 | 0.828 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 844,255 | 844,255 |
Final particle images (no.) | 147,415 | 302,403 |
Map resolution (Å) | 3.17 | 3.23 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 2.0–10.0 | 2.0–13.0 |
Refinement | ||
Initial model used (PDB code) | Closed state of this study | |
Model resolution (Å) | 3.16 | 3.20 |
FSC threshold | 0.143 | 0.143 |
Model resolution range (Å) | 2.0–10.0 | 2.0–13.0 |
Map sharpening B factor (Å2) | −71.6 | −62.8 |
Model composition | ||
Nonhydrogen atoms | 21,056 | 20,934 |
Protein/DNA residues | 2,558/23 | 2,545/23 |
Ligands | 10 | 9 |
B factors (Å2) | ||
Protein/DNA | 77.50/97.75 | 67.41/122.77 |
Ligand | 48.03 | 45.52 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.002 | 0.002 |
Bond angles (°) | 0.537 | 0.560 |
Validation | ||
MolProbity score | 1.77 | 1.73 |
Clashscore | 7.24 | 7.78 |
Poor rotamers (%) | 0.04 | 0.04 |
Ramachandran plot | ||
Favored (%) | 94.55 | 95.59 |
Allowed (%) | 5.45 | 4.41 |
Disallowed (%) | 0 | 0 |
