9H8Q

Eugenol Oxidase (EUGO)from Rhodococcus jostii RHA1, mutant DTT-T425G


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.829341-46% MPD and 0.1 M bis-tris propane
Crystal Properties
Matthews coefficientSolvent content
2.342

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.439α = 89.87
b = 110.197β = 89.34
c = 117.536γ = 68.51
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2024-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9655ESRFMASSIF-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
11.6117.5393.20.0730.090.0520.9959.72.8519315
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)
11.61.6360.10.9061.1320.6690.422.5

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 REPLACEMENTTHROUGHOUT1.6102.754939642531593.180.17830.177280.19774RANDOM20.927
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]
-0.45-0.020.36-0.22-0.120.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.777
r_dihedral_angle_2_deg8.259
r_dihedral_angle_1_deg6.153
r_long_range_B_refined4.899
r_long_range_B_other4.816
r_scangle_other3.561
r_scbond_it2.323
r_scbond_other2.323
r_mcangle_it2.043
r_mcangle_other2.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.777
r_dihedral_angle_2_deg8.259
r_dihedral_angle_1_deg6.153
r_long_range_B_refined4.899
r_long_range_B_other4.816
r_scangle_other3.561
r_scbond_it2.323
r_scbond_other2.323
r_mcangle_it2.043
r_mcangle_other2.043
r_angle_refined_deg1.604
r_mcbond_it1.371
r_mcbond_other1.371
r_angle_other_deg0.554
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms33040
Nucleic Acid Atoms
Solvent Atoms2999
Heterogen Atoms550

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing