- PDB-2xts: Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoc... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2xts
Title
Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus
Components
CYTOCHROME
SULFITE DEHYDROGENASE
Keywords
OXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX / SOX SYSTEM / SULFANE OXIDATION / MOLYBDENUM COFACTOR / HEME / ELECTRON TRANSFER
Function / homology
Function and homology information
molybdenum ion binding / oxidoreductase activity / electron transfer activity / heme binding / metal ion binding Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98 Å / Relative weight: 1
Reflection
Resolution: 1.33→50 Å / Num. obs: 273185 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.8
Reflection shell
Resolution: 1.33→1.4 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0109
refinement
XDS
datareduction
SCALA
datascaling
Auto-Rickshaw
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 1.33→50.01 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.831 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.007 / ESU R Free: 0.006 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1111
803
0.3 %
RANDOM
Rwork
0.10699
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obs
0.107
273185
96.82 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK