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Bovine Xanthine Oxidoreductase Crystallized with oxypurinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 The 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 coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.678 α = 90 b = 123.47 β = 90.89 c = 150.059 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.99 48.43 99.7 0.996 10.6 5 210046
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.11 0.843
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.99 47.72 199435 10629 99.74 0.16515 0.16346 0.1711 0.19667 0.2037 RANDOM 29.898
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 15.529 r_dihedral_angle_3_deg 13.276 r_dihedral_angle_1_deg 6.975 r_long_range_B_refined 5.806 r_long_range_B_other 5.697 r_scangle_other 4.54 r_scbond_it 3.095 r_scbond_other 3.095 r_mcangle_it 3.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 15.529 r_dihedral_angle_3_deg 13.276 r_dihedral_angle_1_deg 6.975 r_long_range_B_refined 5.806 r_long_range_B_other 5.697 r_scangle_other 4.54 r_scbond_it 3.095 r_scbond_other 3.095 r_mcangle_it 3.065 r_mcangle_other 3.065 r_mcbond_it 2.312 r_mcbond_other 2.312 r_angle_refined_deg 1.623 r_angle_other_deg 1.381 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 19980 Nucleic Acid Atoms Solvent Atoms 1815 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing