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Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under reducing conditions (space group P 21 21 21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7A0L
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
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.22 α = 90 b = 124.4 β = 90 c = 125.77 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 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97950 Diamond I24
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 2.12 66.88 100 0.186 0.07 0.997 8.1 8 91505
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 2.12 2.16 100 2.54 0.934 0.363 0.9 8.2
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 2.12 66.88 91421 4563 99.963 0.187 0.1854 0.1895 0.2141 0.2132 46.99
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] 1.57 -1.935 0.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.374 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 15.226 r_dihedral_angle_1_deg 7.574 r_lrange_it 5.123 r_lrange_other 5.09 r_scangle_it 3.251 r_scangle_other 3.25 r_mcangle_it 2.492 r_mcangle_other 2.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.374 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 15.226 r_dihedral_angle_1_deg 7.574 r_lrange_it 5.123 r_lrange_other 5.09 r_scangle_it 3.251 r_scangle_other 3.25 r_mcangle_it 2.492 r_mcangle_other 2.492 r_scbond_it 2.091 r_scbond_other 2.087 r_mcbond_it 1.564 r_mcbond_other 1.564 r_angle_refined_deg 1.451 r_angle_other_deg 1.25 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_other 0.222 r_symmetry_nbd_refined 0.194 r_nbd_refined 0.191 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.07 r_ncsr_local_group_2 0.063 r_ncsr_local_group_4 0.063 r_ncsr_local_group_1 0.06 r_ncsr_local_group_3 0.057 r_ncsr_local_group_6 0.055 r_ncsr_local_group_5 0.054 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 9602 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing