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Urate oxidase complexed with 8-azaxanthine under 2.5 MPa oxygen pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 10 mg/ml urate oxidase, 0.2mg/ml 8-azaxanthine, 50mM Tris, 20mM NaCl, PEG 8000 4-10%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.753 α = 90 b = 96.285 β = 90 c = 105.427 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 277 CCD MARMOSAIC 225 mm CCD mirrors 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.61 50 98.8 0.055 10.9 3.4 52825 52204 1 1 19.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.61 1.67 97.6 0.374 2.15 3 5133
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 rigid body THROUGHOUT 2IBA 1.61 14.96 49475 2658 98.79 0.17622 0.17519 0.1809 0.19509 0.2 RANDOM 21.718
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.75 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_4_deg 7.6 r_dihedral_angle_1_deg 5.971 r_scangle_it 4.056 r_scbond_it 2.461 r_mcangle_it 1.64 r_angle_refined_deg 1.493 r_mcbond_it 0.87 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.75 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_4_deg 7.6 r_dihedral_angle_1_deg 5.971 r_scangle_it 4.056 r_scbond_it 2.461 r_mcangle_it 1.64 r_angle_refined_deg 1.493 r_mcbond_it 0.87 r_nbtor_refined 0.309 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.102 r_metal_ion_refined 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing