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Crystal structure of human D-amino acid oxidase: bound to an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VE9 PDB ENTRY 1VE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 15% PEG 3350, 0.15M POTASSIUM TRICITR TRIS-HCL, pH 7.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.729 α = 90 b = 51.145 β = 110.45 c = 153.294 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE 2005-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON
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 2.49 50 96.8 0.097 11 2.9 46710
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 2.49 2.59 95.4 0.558 2 2.9
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 1VE9 2.49 42.52 44300 2362 96.48 0.24342 0.23893 0.2372 0.3285 0.2244 RANDOM 23.324
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] -1.56 1.04 -0.75 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.537 r_dihedral_angle_3_deg 21.765 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_1_deg 8.53 r_scangle_it 4.235 r_scbond_it 2.827 r_angle_refined_deg 2.665 r_mcangle_it 1.757 r_mcbond_it 1.065 r_nbtor_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.537 r_dihedral_angle_3_deg 21.765 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_1_deg 8.53 r_scangle_it 4.235 r_scbond_it 2.827 r_angle_refined_deg 2.665 r_mcangle_it 1.757 r_mcbond_it 1.065 r_nbtor_refined 0.331 r_nbd_refined 0.275 r_symmetry_hbond_refined 0.206 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.156 r_bond_refined_d 0.028 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10552 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 256
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data scaling