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Crystal structure of human D-amino acid oxidase in complex with hydroxyquinolin-2(1H)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AN9 PDB entry 1AN9
Crystallization Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.063 α = 102.62 b = 82.584 β = 105.43 c = 96.974 γ = 110.79
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 ADSC QUANTUM 315 2008-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.2 50 88.5 0.068 1.7 61073 2
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 1AN9 2.2 10 56486 3049 88.53 0.242 0.23929 0.2469 0.29377 0.2986 RANDOM 46.903
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] -0.87 0.8 -0.95 3.56 0.55 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.436 r_dihedral_angle_4_deg 24.728 r_dihedral_angle_3_deg 20.528 r_scangle_it 6.079 r_dihedral_angle_1_deg 5.784 r_scbond_it 3.479 r_mcangle_it 2.233 r_angle_refined_deg 1.706 r_angle_other_deg 1.373 r_mcbond_it 1.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.436 r_dihedral_angle_4_deg 24.728 r_dihedral_angle_3_deg 20.528 r_scangle_it 6.079 r_dihedral_angle_1_deg 5.784 r_scbond_it 3.479 r_mcangle_it 2.233 r_angle_refined_deg 1.706 r_angle_other_deg 1.373 r_mcbond_it 1.065 r_mcbond_other 0.244 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10932 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement