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Crystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 2.5 kGy)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 20MG/ML UOX IN 50 MM TRIS-ACETATE PH 8.0 SATURATED WITH 9-METHYL URIC ACID UNDER ANAEROBIC CONDITIONS RESERVOIR: 8% PEG 8000, 50 MM TRIS-ACETATE PH 8.0 CRYSTALLIZATION WAS CARRIED OUT ANAEROBICALLY. CRYSTALS WERE EXPOSED TO AIR TO GENERATE THE PEROXIDE
Crystal Properties Matthews coefficient Solvent content 2.9 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.506 α = 90 b = 95.132 β = 90 c = 104.31 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS 6M MIRRORS 2013-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.32 50 100 0.11 8.8 6.6 92669 -1 10.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.37 99.9 0.72 2 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 OTHER THROUGHOUT NONE 1.32 70.29 88023 4635 99.93 0.11178 0.11044 0.127 0.13696 0.1477 RANDOM 15.409
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] -1.01 0.71 0.31
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 60.78 r_sphericity_bonded 16.317 r_long_range_B_refined 7.766 r_long_range_B_other 5.439 r_scangle_other 3.503 r_rigid_bond_restr 3.131 r_mcangle_it 3.037 r_mcangle_other 3.037 r_mcbond_it 2.682 r_mcbond_other 2.681
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 60.78 r_sphericity_bonded 16.317 r_long_range_B_refined 7.766 r_long_range_B_other 5.439 r_scangle_other 3.503 r_rigid_bond_restr 3.131 r_mcangle_it 3.037 r_mcangle_other 3.037 r_mcbond_it 2.682 r_mcbond_other 2.681 r_scbond_it 2.661 r_scbond_other 2.66 r_angle_refined_deg 1.64 r_angle_other_deg 0.855 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2409 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling