Table 1 Data collection and refinement statistics*.
From: A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease
apo hEXOG complex I | apo hEXOG complex II | hEXOG–DNA complex I | hEXOG–DNA complex II | |
|---|---|---|---|---|
PDB | 5T40 | 5T3V | 5T5C | 5T4I |
hEXOG | Wild type | Wild type | H140A | H140A |
Substrate DNA | — | — | 10 bp | 10 bp |
Metal ion | Mg2+ | Mn2+ | Mg2+ | Mn2+ |
Wavelength | 1.0 | 1.89 | 1.0 | 1.89 |
Data collection | ||||
Space group | P 21 | P 21 | P 21 21 21 | P 21 21 21 |
Cell dimensions | ||||
a, b, c (Å) | 73.37, 83.73, 75.00 | 73.34, 83.44, 74.77 | 73.50, 80.27, 139.18 | 73.51, 79.72, 138.87 |
α, β, γ (°) | 90.00, 113.54, 90.00 | 90, 113.42, 90.00 | 90, 90, 90 | 90, 90, 90 |
Resolution (Å) | 34.7–1.81 (1.83–1.81)† | 49.7–2.6 (2.66–2.60) | 39.2–1.85 (1.87–1.85) | 40.0–2.39 (2.45–2.39) |
Rsym or Rmerge | 0.052 (0.814) | 0.058 (0.337) | 0.08 (1.0) | 0.114 (0.638) |
I/σI | 25.8 (1.54) | 21.7 (2.3) | 31.5 (1.56) | 24.8 (2.4) |
CC† | 1.000 (0.926) | 0.999 (0.989) | 1.000 (0.957) | 0.994 (0.994) |
Completeness (%) | 98.10 (97.8) | 95.7 (93.3) | 99.9 (99.1) | 99.5 (97.4) |
Redundancy | 3.6 (3.4) | 3.6 (3.6) | 7.2 (6.3) | 5.7 (4.4) |
Molecular replacement | ||||
Model | 3ISM | 5T40 | 5T40 | 5T5C |
LLG | 592.97 | 518.40 | 686.22 | 13,776.6 |
TFZ | 18.2 | 42.6 | 34.6 | 57.2 |
Refinement | ||||
Resolution (Å) | 34.7–1.81 | 49.7–2.6 | 39.23–1.85 | 40.03–2.39 |
No. reflections | 74,273 | 24,370 | 70,421 | 32,854 |
Rwork/Rfree | 16.1/18.7 | 17.6/22.4 | 18.7/21.8 | 19.1/22.9 |
No. of atoms | ||||
Protein | 9,552 | 9,552 | 9,465 | 9,464 |
Ligand/ion | 22 | 12 | 1,148 | 1,144 |
Water | 440 | 81 | 272 | 57 |
B-factors | ||||
Protein | 39.37 | 63.54 | 58.41 | 63.16 |
Ligand/ion | 57.95 | 127.37 | 32.09 | 57.31 |
Water | 44.36 | 48.30 | 46.26 | 47.82 |
r.m.s.d. | ||||
Bond lengths (Å) | 0.004 | 0.003 | 0.003 | 0.003 |
Bond angles (°) | 0.7 | 0.483 | 0.59 | 0.53 |
