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urate oxidase under 2.0 MPa 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 VAPOR DIFFUSION, SITTING DROP 10.5 298 urate oxidase 8.5mg/ml, sodium carbonate 10mM, 8-azaxanthin 0.2mg/ml, PEG 8000 7%
, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.189 α = 90 b = 96.034 β = 90 c = 105.212 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 IMAGE PLATE MARRESEARCH 2002-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 0.964 LURE DW32
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 1.75 99 99.9 0.055 13.3 41239 1 1 18.9
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 1.75 1.81 99.8 0.346 4076
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 14.77 39086 2074 99.94 0.16642 0.16528 0.1646 0.18779 0.1887 RANDOM 21.03
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 37.143 r_dihedral_angle_3_deg 13.338 r_dihedral_angle_4_deg 8.033 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.239 r_scbond_it 2.555 r_mcangle_it 1.678 r_angle_refined_deg 1.476 r_mcbond_it 0.976 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.143 r_dihedral_angle_3_deg 13.338 r_dihedral_angle_4_deg 8.033 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.239 r_scbond_it 2.555 r_mcangle_it 1.678 r_angle_refined_deg 1.476 r_mcbond_it 0.976 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.104 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_refined 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 198 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection