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Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FIQ PDB entry 1FIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7.2 298 PEG 8000, pH 7.2, batch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.298 α = 96.88 b = 133.176 β = 93.11 c = 142.633 γ = 90.02
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2008-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 141.42 119504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.668 5403
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1FIQ 2.6 33.08 119504 6008 72.66 0.217 0.214 0.2178 0.268 0.2706 RANDOM 13.895
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] -0.45 -0.07 0.03 -1.89 0.68 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.84 r_dihedral_angle_4_deg 20.034 r_dihedral_angle_3_deg 17.897 r_dihedral_angle_1_deg 6.806 r_scangle_it 2.544 r_angle_refined_deg 1.659 r_scbond_it 1.553 r_mcangle_it 1.034 r_mcbond_it 0.615 r_symmetry_vdw_refined 0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.84 r_dihedral_angle_4_deg 20.034 r_dihedral_angle_3_deg 17.897 r_dihedral_angle_1_deg 6.806 r_scangle_it 2.544 r_angle_refined_deg 1.659 r_scbond_it 1.553 r_mcangle_it 1.034 r_mcbond_it 0.615 r_symmetry_vdw_refined 0.385 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37670 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 400
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction