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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, 665 kGy)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 LIKE PDB CODE 4CW2, pH 8
Crystal Properties Matthews coefficient Solvent content 2.9 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.498 α = 90 b = 95.157 β = 90 c = 104.415 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 1.34 50 100 0.1 9.4 6.5 88740 -1 7.15
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 1.34 1.39 99.9 0.73 2.1 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 1.34 70.33 84283 4451 99.93 0.11037 0.10917 0.1265 0.13399 0.147 RANDOM 15.952
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] 0.5 -0.28 -0.22
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.464 r_sphericity_bonded 13.982 r_mcangle_it 2.309 r_scbond_it 2.229 r_rigid_bond_restr 2.187 r_mcbond_it 1.997 r_mcbond_other 1.997 r_angle_refined_deg 1.5 r_angle_other_deg 0.807 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.464 r_sphericity_bonded 13.982 r_mcangle_it 2.309 r_scbond_it 2.229 r_rigid_bond_restr 2.187 r_mcbond_it 1.997 r_mcbond_other 1.997 r_angle_refined_deg 1.5 r_angle_other_deg 0.807 r_chiral_restr 0.093 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_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2409 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling