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Urate oxidase under 2.0 MPa 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 VAPOR DIFFUSION, HANGING DROP 8 298 4MG/ML URATE OXIDASE, 8-AZAXANTHINE 0.2MG/ML, TRIS 50MM, PEG 8000 2-5%, NACL 100MM, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.502 α = 90 b = 96.583 β = 90 c = 106.005 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 MAR scanner 345 mm plate MIRRORS 2003-03-15 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 20 82.5 0.049 34588 1 16.39
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 44.3 0.049 1813
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.78 14.84 1 33398 1677 83.85 0.166 0.164 0.1641 0.201 0.2008 RANDOM 20.84
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 38.309 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_4_deg 12.77 r_dihedral_angle_1_deg 6.084 r_scangle_it 4.079 r_scbond_it 2.533 r_mcangle_it 1.607 r_angle_refined_deg 1.501 r_mcbond_it 0.846 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_4_deg 12.77 r_dihedral_angle_1_deg 6.084 r_scangle_it 4.079 r_scbond_it 2.533 r_mcangle_it 1.607 r_angle_refined_deg 1.501 r_mcbond_it 0.846 r_nbtor_refined 0.304 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.104 r_metal_ion_refined 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2362 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection