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Urate oxidase under 1.5 MPa / 15 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 58.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.219 α = 90 b = 96.255 β = 90 c = 105.5 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 0.05 33.8 4.9 40577 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 93.5 0.276 4.5 4.2 3832
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 38472 2038 97.85 0.17023 0.16897 0.1679 0.19424 0.1925 RANDOM 22.596
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.998 r_dihedral_angle_3_deg 12.124 r_dihedral_angle_4_deg 8.598 r_dihedral_angle_1_deg 6.011 r_scangle_it 4.362 r_scbond_it 2.626 r_mcangle_it 1.769 r_angle_refined_deg 1.441 r_mcbond_it 0.941 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.998 r_dihedral_angle_3_deg 12.124 r_dihedral_angle_4_deg 8.598 r_dihedral_angle_1_deg 6.011 r_scangle_it 4.362 r_scbond_it 2.626 r_mcangle_it 1.769 r_angle_refined_deg 1.441 r_mcbond_it 0.941 r_nbtor_refined 0.311 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.106 r_metal_ion_refined 0.053 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 173 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling