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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 C 2 2 21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 291.15 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 8% PGA-LM, 0.3M KBr, 0.1M Tris-HCl pH 7.8 using a 1:1 ratio. Crystals were then 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 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.51 α = 90 b = 125.99 β = 90 c = 240.68 γ = 90
Symmetry Space Group C 2 2 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 1.86 77.06 100 0.116 0.033 0.999 12.1 13.8 135367
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 1.86 1.89 100 0.403 0.11 0.3 0.5 14.2
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 1.86 77.058 135131 6736 99.858 0.174 0.1719 0.1796 0.2064 0.2098 45.567
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] 0.812 -1.637 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_3_deg 14.517 r_dihedral_angle_4_deg 13.776 r_dihedral_angle_1_deg 7.235 r_lrange_it 5.518 r_lrange_other 5.41 r_scangle_it 3.007 r_scangle_other 3.007 r_mcangle_it 2.026 r_mcangle_other 2.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_3_deg 14.517 r_dihedral_angle_4_deg 13.776 r_dihedral_angle_1_deg 7.235 r_lrange_it 5.518 r_lrange_other 5.41 r_scangle_it 3.007 r_scangle_other 3.007 r_mcangle_it 2.026 r_mcangle_other 2.026 r_scbond_it 1.993 r_scbond_other 1.991 r_angle_refined_deg 1.483 r_mcbond_it 1.392 r_mcbond_other 1.39 r_angle_other_deg 1.28 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.177 r_nbd_other 0.177 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.127 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.018 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9641 Nucleic Acid Atoms Solvent Atoms 747 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing