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Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under oxidising conditions (space group P 21 21 21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 His6-tagged GgUOX at approx. 22 mg/ml in 50 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM TCEP-HCl was incubated with a 20-fold molar excess of AZA. Crystals were obtained by mixing the protein with 0.8M K/Na tartrate tetrahydrate, 0.1 M HEPES pH 7.5 using a 1:1 ratio. Crystals were transferred into cryoprotective solutions supplemented with 100 mM H2O2 and devoid of the TCEP-HCl reducing agent for approximately 15 minutes prior to cryocooling in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.775 α = 90 b = 124.859 β = 90 c = 128.265 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2021-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97948 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.89 78.89 100 0.17 0.048 0.998 7.6 13.5 131041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 98.1 0.405 0.123 0.253 0.3 11.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.89 78.888 128034 6233 97.677 0.189 0.1881 0.1948 0.2145 0.2191 41.869
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] -0.517 -0.129 0.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_3_deg 15.352 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_1_deg 7.238 r_lrange_it 4.774 r_lrange_other 4.773 r_scangle_it 2.722 r_scangle_other 2.722 r_mcangle_it 2 r_mcangle_other 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_3_deg 15.352 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_1_deg 7.238 r_lrange_it 4.774 r_lrange_other 4.773 r_scangle_it 2.722 r_scangle_other 2.722 r_mcangle_it 2 r_mcangle_other 2 r_scbond_it 1.718 r_scbond_other 1.718 r_angle_refined_deg 1.414 r_mcbond_it 1.259 r_mcbond_other 1.259 r_angle_other_deg 1.25 r_symmetry_xyhbond_nbd_refined 0.299 r_nbd_other 0.219 r_nbd_refined 0.194 r_symmetry_nbd_other 0.176 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.1 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.067 r_ncsr_local_group_4 0.059 r_ncsr_local_group_1 0.055 r_ncsr_local_group_5 0.055 r_ncsr_local_group_3 0.052 r_ncsr_local_group_2 0.051 r_ncsr_local_group_6 0.047 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9620 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing