- PDB-3x16: Crystal structure of the catalase-peroxidase KatG W78F mutant fro... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3x16
Title
Crystal structure of the catalase-peroxidase KatG W78F mutant from Synechococcus elongatus PCC7942
Components
Catalase-peroxidase
Keywords
OXIDOREDUCTASE / peroxidase / catalase subfamily / heme b Fe / cross-link / Trp-Tyr-Met adduct
Function / homology
Function and homology information
catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.65→50 Å / Num. obs: 35801 / % possible obs: 99.8 % / Redundancy: 12 % / Rmerge(I) obs: 0.162 / Χ2: 17.889 / Net I/σ(I): 12.4
Reflection shell
Diffraction-ID: 1 / Rejects: 0
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Rpim(I) all
Rrim(I) all
Χ2
% possible all
2.65-2.74
11.1
0.491
6653
0.143
0.513
2.885
99.4
2.74-2.85
11.1
0.399
6703
0.116
0.416
3.971
99.6
2.85-2.98
11.1
0.31
6738
0.09
0.323
4.334
99.8
2.98-3.14
11.2
0.251
6731
0.072
0.261
6.119
99.8
3.14-3.34
11.3
0.193
6705
0.055
0.201
9.678
99.8
3.34-3.6
11.6
0.161
6740
0.045
0.168
14.958
99.8
3.6-3.96
12
0.139
6740
0.039
0.145
19.32
99.9
3.96-4.53
12.4
0.143
6751
0.04
0.148
27.516
100
4.53-5.71
13.3
0.16
6790
0.044
0.166
31.634
100
5.71-50
14.4
0.116
6805
0.032
0.121
44.829
99.5
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
5.7.0032
refinement
PDB_EXTRACT
3.15
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
MOLREP
phasing
Refinement
Resolution: 2.65→42.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.744 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2538
1784
5 %
RANDOM
Rwork
0.1966
-
-
-
obs
0.1995
33798
99.39 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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