7BX9

Purification, characterization and X-ray structure of YhdA-type azoreductase from Bacillus velezensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GSW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2890.05 M Potassium phosphate monobasic, 20% w/v Polyethylene glycol 8,000
Crystal Properties
Matthews coefficientSolvent content
3.0259.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.43α = 90
b = 102.47β = 90
c = 65.73γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3836.711000.996105.45100811.69
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.410.7922

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2GSW1.3830.971.3551006269399.940.13170.13060.151518.53
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.6764
f_angle_d0.7756
f_chiral_restr0.0711
f_plane_restr0.0053
f_bond_d0.0047
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1297
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms66

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing