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Urate oxidase under 0.8 MPa / 8 bars pressure of xenon
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, 2 mg/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 58.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.276 α = 90 b = 96.327 β = 90 c = 105.495 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 CCD ADSC QUANTUM 210r MIRRORS 2008-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.979 ESRF BM16
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 1.749 30 90.7 0.061 24.2 5.3 37664 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 1.749 1.81 95.1 0.447 3 5.2
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 1.749 14.99 35747 1893 90.69 0.17409 0.17292 0.1726 0.19586 0.1953 RANDOM 24.714
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.703 r_dihedral_angle_3_deg 12.557 r_dihedral_angle_4_deg 8.905 r_dihedral_angle_1_deg 6.034 r_scangle_it 4.354 r_scbond_it 2.637 r_mcangle_it 1.766 r_angle_refined_deg 1.398 r_mcbond_it 0.947 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.703 r_dihedral_angle_3_deg 12.557 r_dihedral_angle_4_deg 8.905 r_dihedral_angle_1_deg 6.034 r_scangle_it 4.354 r_scbond_it 2.637 r_mcangle_it 1.766 r_angle_refined_deg 1.398 r_mcbond_it 0.947 r_nbtor_refined 0.31 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.103 r_metal_ion_refined 0.054 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 153 Heterogen Atoms 13
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling