6RGT

Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CW0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29320 MG/ML UOX T57A IN 50 MM TRIS-HCL PH 8.0 SATURATED WITH 9-METHYL URIC ACID, 8% PEG 8000 - CRYSTALS GROWN ANAEROBICALLY
Crystal Properties
Matthews coefficientSolvent content
2.8857.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.291α = 90
b = 95.116β = 90
c = 104.503γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD SAPPHIRE CCD2017-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION NOVA1.54

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
11.614.0299.80.1040.1170.0510.9969.34.952248
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)
11.61.6999.71.4111.7380.9910.3610.93

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4CW01.614.0249561268399.680.162950.161520.18905RANDOM17.011
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]
1.6-0.57-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.089
r_dihedral_angle_4_deg15.705
r_dihedral_angle_3_deg12.634
r_long_range_B_refined7.663
r_dihedral_angle_1_deg7.166
r_long_range_B_other6.49
r_scangle_other3.272
r_mcangle_it2.903
r_mcangle_other2.903
r_scbond_it2.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.089
r_dihedral_angle_4_deg15.705
r_dihedral_angle_3_deg12.634
r_long_range_B_refined7.663
r_dihedral_angle_1_deg7.166
r_long_range_B_other6.49
r_scangle_other3.272
r_mcangle_it2.903
r_mcangle_other2.903
r_scbond_it2.053
r_scbond_other2.053
r_mcbond_it1.841
r_mcbond_other1.815
r_angle_refined_deg1.596
r_angle_other_deg1.459
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2404
Nucleic Acid Atoms
Solvent Atoms597
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing