7PBG

4-ethylphenol oxidase from Gulosibacter chungangensis: native structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FXD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1 M Trizma pH 8.0, 24% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.4348

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.134α = 90
b = 96.08β = 115.65
c = 87.636γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.999869SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.644.2394.50.0830.0920.0390.9969.84.9140211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6386.40.6420.7380.3530.713.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5FXD1.644.23133003697594.270.18220.18090.2066RANDOM21.958
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]
0.630.54-1.620.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.36
r_dihedral_angle_4_deg22.026
r_dihedral_angle_3_deg11.928
r_dihedral_angle_1_deg6.681
r_angle_refined_deg1.655
r_angle_other_deg1.535
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.36
r_dihedral_angle_4_deg22.026
r_dihedral_angle_3_deg11.928
r_dihedral_angle_1_deg6.681
r_angle_refined_deg1.655
r_angle_other_deg1.535
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8200
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms108

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing