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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 C 2 2 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 7.8 291.15 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
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.195 α = 90 b = 125.475 β = 90 c = 238.581 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 PILATUS 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 1.713 81.502 98.9 0.082 0.042 0.998 8.7 4.4 169907
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 1.713 1.742 98.2 1.418 0.768 0.345 0.8 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 1.713 81.502 168411 8247 98.014 0.182 0.1815 0.1877 0.2008 0.208 35.416
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] 0.476 -0.665 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.311 r_dihedral_angle_4_deg 14.195 r_dihedral_angle_3_deg 13.472 r_dihedral_angle_1_deg 6.946 r_lrange_it 6.171 r_lrange_other 6.009 r_scangle_it 1.612 r_scangle_other 1.612 r_angle_refined_deg 1.362 r_angle_other_deg 1.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.311 r_dihedral_angle_4_deg 14.195 r_dihedral_angle_3_deg 13.472 r_dihedral_angle_1_deg 6.946 r_lrange_it 6.171 r_lrange_other 6.009 r_scangle_it 1.612 r_scangle_other 1.612 r_angle_refined_deg 1.362 r_angle_other_deg 1.319 r_mcangle_it 1.241 r_mcangle_other 1.241 r_scbond_it 1.051 r_scbond_other 1.051 r_mcbond_it 0.741 r_mcbond_other 0.741 r_nbd_refined 0.193 r_symmetry_nbd_refined 0.193 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.069 r_ncsr_local_group_3 0.069 r_ncsr_local_group_6 0.066 r_ncsr_local_group_1 0.063 r_ncsr_local_group_2 0.061 r_ncsr_local_group_5 0.061 r_ncsr_local_group_4 0.056 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 9613 Nucleic Acid Atoms Solvent Atoms 933 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing