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Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 20 MG/ML UOX T57A IN 50 MM TRIS-HCL PH 8.0
SATURATED WITH 9-METHYL URIC ACID, 8% PEG 8000 - CRYSTALS GROWN ANAEROBICALLY
Crystal Properties Matthews coefficient Solvent content 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.291 α = 90 b = 95.116 β = 90 c = 104.503 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 CCD OXFORD SAPPHIRE CCD 2017-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 14.02 99.8 0.104 0.117 0.051 0.996 9.3 4.9 52248
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 99.7 1.411 1.738 0.991 0.361 0.9 3
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 FOURIER SYNTHESIS THROUGHOUT 4CW0 1.6 14.02 49561 2683 99.68 0.16295 0.16152 0.1747 0.18905 0.1993 RANDOM 17.011
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] 1.6 -0.57 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.089 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_3_deg 12.634 r_long_range_B_refined 7.663 r_dihedral_angle_1_deg 7.166 r_long_range_B_other 6.49 r_scangle_other 3.272 r_mcangle_it 2.903 r_mcangle_other 2.903 r_scbond_it 2.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.089 r_dihedral_angle_4_deg 15.705 r_dihedral_angle_3_deg 12.634 r_long_range_B_refined 7.663 r_dihedral_angle_1_deg 7.166 r_long_range_B_other 6.49 r_scangle_other 3.272 r_mcangle_it 2.903 r_mcangle_other 2.903 r_scbond_it 2.053 r_scbond_other 2.053 r_mcbond_it 1.841 r_mcbond_other 1.815 r_angle_refined_deg 1.596 r_angle_other_deg 1.459 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling REFMAC phasing