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Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7 298 PEG 8000, DTT, pyrophosphate, phosphate, TRIS, pH 7.0, batch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.187 α = 90 b = 73.794 β = 98.87 c = 146.498 γ = 90
Symmetry Space Group P 1 21 1
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 2007-05-15 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 2.3 144.34 120613 114520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1FIQ 2.3 144.34 120613 114520 6093 96.25 0.197 0.194 0.1969 0.263 0.2658 RANDOM 22.698
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] -2.04 1.13 -0.55 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.172 r_dihedral_angle_4_deg 19.786 r_dihedral_angle_3_deg 18.141 r_dihedral_angle_1_deg 9.919 r_scangle_it 2.888 r_scbond_it 1.878 r_angle_refined_deg 1.798 r_mcangle_it 1.228 r_angle_other_deg 1.078 r_mcbond_it 0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.172 r_dihedral_angle_4_deg 19.786 r_dihedral_angle_3_deg 18.141 r_dihedral_angle_1_deg 9.919 r_scangle_it 2.888 r_scbond_it 1.878 r_angle_refined_deg 1.798 r_mcangle_it 1.228 r_angle_other_deg 1.078 r_mcbond_it 0.743 r_symmetry_vdw_refined 0.379 r_symmetry_hbond_refined 0.324 r_symmetry_vdw_other 0.297 r_xyhbond_nbd_refined 0.222 r_nbd_refined 0.22 r_nbd_other 0.212 r_nbtor_refined 0.178 r_chiral_restr 0.152 r_mcbond_other 0.143 r_nbtor_other 0.091 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18785 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 201
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction At data scaling