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Urate oxidase under 2 MPa / 20 bars pressure of nitrous oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBA PDB entry 2IBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH 8.5 298 10-15 mg/ml urate oxidase, 2mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.98 58.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.238 α = 90 b = 96.26 β = 90 c = 105.543 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 298 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2008-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.954 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 30 97.8 0.046 35.4 4.8 40615 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 97.1 0.222 5.3 4.2 3982
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 PDB entry 2IBA 1.75 14.98 38482 2044 97.83 0.16787 0.16688 0.1656 0.18619 0.185 RANDOM 22.847
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 36.406 r_dihedral_angle_3_deg 12.142 r_dihedral_angle_4_deg 9.614 r_dihedral_angle_1_deg 6.057 r_scangle_it 4.453 r_scbond_it 2.67 r_mcangle_it 1.792 r_angle_refined_deg 1.425 r_mcbond_it 0.945 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.406 r_dihedral_angle_3_deg 12.142 r_dihedral_angle_4_deg 9.614 r_dihedral_angle_1_deg 6.057 r_scangle_it 4.453 r_scbond_it 2.67 r_mcangle_it 1.792 r_angle_refined_deg 1.425 r_mcbond_it 0.945 r_nbtor_refined 0.311 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.106 r_metal_ion_refined 0.079 r_bond_refined_d 0.013 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 2362 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling