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Crystal Structure of Human D-Amino Acid Oxidase in complex with o-aminobenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DU8 PDB ENTRY 2DU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 10% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.392 α = 90 b = 185.042 β = 90 c = 51.577 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 297 IMAGE PLATE RIGAKU RAXIS VII 2006-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.0
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 2.6 50 98.8 0.085 9 3.1 45267
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) 2.6 2.69 98.2 0.331 2.5
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2DU8 2.6 50 42932 2287 98.79 0.21186 0.21186 0.2101 0.24435 0.218 RANDOM 39.917
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] -0.07 -1.03 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.984 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 17.136 r_dihedral_angle_1_deg 5.261 r_scangle_it 2.228 r_angle_refined_deg 1.4 r_scbond_it 1.306 r_mcangle_it 1.243 r_mcbond_it 0.688 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.984 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 17.136 r_dihedral_angle_1_deg 5.261 r_scangle_it 2.228 r_angle_refined_deg 1.4 r_scbond_it 1.306 r_mcangle_it 1.243 r_mcbond_it 0.688 r_nbtor_refined 0.31 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.205 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 10932 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing