Data collection statistics | 8‐oxodG:dCTP complex | AP:dG complex | 8‐oxodG editing complex |
---|---|---|---|
Space group | P2_{1}2_{1}2_{1} | P2_{1} | P1 |
Unit cell dimensions: | |||
a, b, c (Å) | 80.8, 118.6, 127.2 | 131.9, 122.2, 165.4 | 73.1, 124.7, 126.5 |
α, β, γ (deg) | 90, 90, 90 | 90, 96.8, 90 | 118.8, 89.7, 106.8 |
Unique reflections | 30441 | 137338 | 148642 |
Resolution (highest shell) (Å) | 46.1–2.8 (2.9–2.8) | 47.1–2.7 (2.8–2.7) | 50.0–2.35 (2.43–2.35) |
R_{sym} (highest shell) | 0.116 (0.616) | 0.113 (0.434) | 0.045 (0.373) |
Completeness (highest shell) (%) | 99.9 (100.0) | 94.7 (73.3) | 98.0 (97.1) |
Average redundancy | 4.5 | 4.8 | 6.3 |
〈I〉/〈σ(I)〉 (highest shell) | 11.0 (1.8) | 19.1 (1.8) | 10.1 (2.1) |
Refinement statistics | |||
Number of reflections used in refinement | 28854 | 130465 | |
Final R (R_{free}) | 20.4 (27.1) | 21.5 (28.8) | |
Deviations from ideal values in | |||
Bond distances (Å) | 0.016 | 0.013 | |
Bond angles (deg) | 1.87 | 1.54 | |
Torsion angles (deg) | 7.5 | 6.5 | |
Chiral centers (Å^{3}) | 0.09 | 0.11 | |
Planar groups (Å) | 0.006 | 0.005 | |
Ramachandran statistics (%) | 88.0/10.9/1.0/0.1 | 86.7/12.1/0.8/0.4 | |
Model contents (number of atoms) | |||
Protein | 7356 | 29460 | |
DNA | 652 | 2692 | |
Waters | 84 | 535 | |
Bound metals | 3 | 8 | |
Other ligands | 28 | 61 |
R_{sym}=∑_{hkl}∑_{i} ∣I_{i}−〈I〉∣/∑_{i} 〈I〉, where I_{i} is the ith measurement and 〈I〉 is the weighted mean of all measurements of I. 〈I〉/〈sigI〉 indicates the average of the intensity divided by its standard deviation. Numbers in parentheses refer to the respective highest resolution data shell in each dataset. R_{cryst}=∑∣∣F_{o}∣−∣F_{c}∣∣/∑∣F_{o}∣ where F_{o} and F_{c} are the observed and calculated structure factor amplitudes. R_{free} same as R_{cryst} for 5% of the data randomly omitted from refinement. Ramachandran statistics indicate the fraction of residues in the most favored, additionally allowed and generously allowed and disallowed regions of the Ramachandran diagram as defined by PROCHECK (Laskowski et al, 1993).