9GJ0

Eugenol Oxidase (EUGO)from Rhodococcus jostii RHA1, mutant B1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.2 M Ammonium Sulphate, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.450

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.77α = 90
b = 109.77β = 90
c = 244.985γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2024-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.969ESRFMASSIF-1

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
12.76244.99970.1280.1310.030.99918.419.243581
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)
12.762.861003.4753.5760.8390.38917.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.7695.0641342218197.060.208980.205910.26558RANDOM100.651
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]
-0.54-0.27-0.541.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.631
r_long_range_B_refined16.534
r_long_range_B_other16.534
r_scangle_other13.131
r_mcangle_it12.837
r_mcangle_other12.836
r_dihedral_angle_2_deg9.957
r_mcbond_it8.996
r_mcbond_other8.995
r_scbond_it8.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.631
r_long_range_B_refined16.534
r_long_range_B_other16.534
r_scangle_other13.131
r_mcangle_it12.837
r_mcangle_other12.836
r_dihedral_angle_2_deg9.957
r_mcbond_it8.996
r_mcbond_other8.995
r_scbond_it8.857
r_scbond_other8.856
r_dihedral_angle_1_deg6.776
r_angle_refined_deg1.426
r_angle_other_deg0.505
r_chiral_restr0.068
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12256
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing