8J79

Bovine Xanthine Oxidoreductase Crystallized with oxypurinol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FO4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293The enzyme solution was exchanged buffer into 50 mM Tris-HCl pH 7.4 and diluted with 50 mM Tris-HCl pH 7.4, 5 mM DTT, 100 micro M oxypurinol, and 30% glycerol to a concentration of 8.6 mg/ml. The precipitant solution contained 50 mM potassium phosphate pH 6.0, 5 mM DTT, 0.2 mM EDTA, 100 micro M oxypurinol, 30% glycerol and 14%-15% PEG 4000. 10 micro L enzyme solution and 10 micro L reservoir solution were mixed on siliconized glass plates and kept in the dark at 20 C for 5 days.
Crystal Properties
Matthews coefficientSolvent content
2.7354.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.678α = 90
b = 123.47β = 90.89
c = 150.059γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9948.4399.70.99610.65210046
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.110.843

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 REPLACEMENTTHROUGHOUT1.9947.721994351062999.740.165150.163460.19667RANDOM29.898
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.823
r_dihedral_angle_4_deg15.529
r_dihedral_angle_3_deg13.276
r_dihedral_angle_1_deg6.975
r_long_range_B_refined5.806
r_long_range_B_other5.697
r_scangle_other4.54
r_scbond_it3.095
r_scbond_other3.095
r_mcangle_it3.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.823
r_dihedral_angle_4_deg15.529
r_dihedral_angle_3_deg13.276
r_dihedral_angle_1_deg6.975
r_long_range_B_refined5.806
r_long_range_B_other5.697
r_scangle_other4.54
r_scbond_it3.095
r_scbond_other3.095
r_mcangle_it3.065
r_mcangle_other3.065
r_mcbond_it2.312
r_mcbond_other2.312
r_angle_refined_deg1.623
r_angle_other_deg1.381
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms19980
Nucleic Acid Atoms
Solvent Atoms1815
Heterogen Atoms248

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing