Table 4 The statistics of X-ray structure data collection, processing and structure refinement and validation of AsfvTop2 ATPase/MgAMP-PNP in reduced and oxidized states
From: A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase
| Â | Reduced | Oxidized |
|---|---|---|
PDB code | 8JA2 | 8JA1 |
Data Collection | ||
Space group | P6122 | P6122 |
Unit cell dimensions | ||
a, b, c (Ã…) | 85.92, 85.92, 212.01 | 85.76, 85.76, 212.30 |
α, β, γ (°) | 90, 90, 120 | 90.00, 90.00, 120.00 |
Resolution (Å) | 43.21–1.73 (1.82–1.73)a | 43.18–1.14 (1.20–1.14)a |
Rmerge | 0.069 (0.404)a | 0.098 (1.210)a |
I/σI | 18.6 (4.9)a | 15.1 (2.1)a |
Completeness (%) | 99.0 (98.7)a | 99.8 (98.6)a |
Multiplicity | 8.6 (8.4)a | 20.1(13.2)a |
Total reflections / Unique reflections | 417449 (58802)a / 48808 (6982)a | 3356924 (312727)a / 166668 (23634)a |
CC½ | 0.999 (0.934)a | 0.999 (0.696)a |
Search model (PDB) | 1PVG55 | Reduced form (8JA2) |
Structure refinement statistics | ||
Rwork/Rfree | 0.1979 / 0.2163 | 0.1838 / 0.1870 |
No. of atoms | ||
Protein | 3099 | 3078 |
AMP-PNP/Mg2+ | 31 / 1 | 31 / 1 |
Water | 227 | 352 |
B-factors (Ã…2)b | ||
Protein | 21.4 | 21.23 |
AMP-PNP/Mg2+ | 12.3 / 12.6 | 9.0 / 7.4 |
Water | 25.5 | 21.5 |
r.m.s. deviations | ||
Bond lengths (Ã…) | 0.05 | 0.007 |
Bond angles (°) | 1.703 | 1.037 |
Ramachandran plot (%)c | ||
favored region | 98.17 | 97.61 |
allowed region | 1.83 | 2.39 |
disallowed region | 0 | 0 |