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

 

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 (Ã…)

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

  1. aNumbers in parenthesis indicate the values in the highest resolution shell.
  2. bAverage B-factor calculated using the average B script in PyMOL Molecular Graphic System (Version 2.2.2).
  3. cRamachandran statistics generated from Phenix v.1.1982.