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Crystal structure of xanthine oxidase in complex with lumazine
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 2.63 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.19 α = 90 b = 73.491 β = 98.68 c = 146.505 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 MARMOSAIC 325 mm CCD APS BEAMLINE SGX PHARMACEUTICALS 2007-06-15 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) 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 2.2 50 98.7 0.197 5 140747 13.1
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 2.2 2.257 96.1 1.7
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 2.2 50 140747 7052 98.71 0.201 0.197 0.1992 0.267 0.268 RANDOM 29.464
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] -2.54 1.16 0.08 2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.121 r_dihedral_angle_4_deg 19.318 r_dihedral_angle_3_deg 18.192 r_dihedral_angle_1_deg 7.967 r_scangle_it 4.007 r_scbond_it 2.664 r_angle_refined_deg 1.96 r_mcangle_it 1.609 r_mcbond_it 1.001 r_metal_ion_refined 0.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.121 r_dihedral_angle_4_deg 19.318 r_dihedral_angle_3_deg 18.192 r_dihedral_angle_1_deg 7.967 r_scangle_it 4.007 r_scbond_it 2.664 r_angle_refined_deg 1.96 r_mcangle_it 1.609 r_mcbond_it 1.001 r_metal_ion_refined 0.611 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.29 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.205 r_chiral_restr 0.129 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18872 Nucleic Acid Atoms Solvent Atoms 1232 Heterogen Atoms 203
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling