5FXP

Crystal structure of eugenol oxidase in complex with vanillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VAOPDB ENTRY 2VAO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1824% PEG6000, 0.1 M TRIS/HCL PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.1642.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.92α = 90
b = 97.45β = 90
c = 180.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXEL2015-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID13ESRFID13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.666.1691.60.147.73.929395
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.7480.40.422.22.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VAO2.690.1127913141790.950.183920.180050.26163RANDOM24.225
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]
0.582.23-2.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.952
r_dihedral_angle_4_deg19.864
r_dihedral_angle_3_deg15.428
r_dihedral_angle_1_deg6.605
r_mcangle_it2.147
r_angle_refined_deg1.545
r_scbond_it1.538
r_mcbond_it1.272
r_mcbond_other1.272
r_angle_other_deg0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.952
r_dihedral_angle_4_deg19.864
r_dihedral_angle_3_deg15.428
r_dihedral_angle_1_deg6.605
r_mcangle_it2.147
r_angle_refined_deg1.545
r_scbond_it1.538
r_mcbond_it1.272
r_mcbond_other1.272
r_angle_other_deg0.993
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8243
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing