Table 2 Cryo-EM data collection, model refinement and validation statistics for hOGG1K249Q bound to the NCP-8-oxodGuo-137 (EMDB-19870, PDB: 9eoz)
From: Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles
Data collection and processing | Dataset 1 | Dataset 2 |
|---|---|---|
Magnification | 130000x | 130000x |
Voltage (kV) | 300 | 300 |
Electron exposure (e–/Å2) | 43.76 | 39.35 |
Defocus range (μm) | −1.1 to −2.9 | −1.1 to −2.9 |
Pixel size (Å) | 1.045 | 1.045 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 1,134,348 | |
Final particle images (no.) | 66,370 | |
Map resolution (Å) | 3.1 | |
FSC threshold | 0.143 | |
Refinement | ||
Initial model used PDB | 1 ebm, 3 lz0 | |
Model composition | ||
Non-hydrogen atoms | 14108 | |
Protein residues | 1033 | |
Nucleotide | 288 | |
B factor (Å2) | ||
Protein | 105.69 | |
Nucleotide | 144.25 | |
RMSDs | ||
Bond lengths (Å) | 0.006 | |
Bond angles (°) | 0.649 | |
Validation | ||
MolProbity score | 1.31 | |
Clashscore | 4.58 | |
Poor rotamers (%) | 0.58 | |
Ramachandran plot | ||
Favored (%) | 97.62 | |
Allowed (%) | 2.38 | |
Disallowed (%) | 0.00 | |
