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Crystal Structure of Human D-Amino Acid Oxidase: Substrate-Free Holoenzyme
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 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.652 α = 90 b = 181.727 β = 90 c = 50.815 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 100 IMAGE PLATE RIGAKU RAXIS VII 2006-10-24 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 2.9 50 97.3 0.102 5.9 3.8 31102
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) 2.9 3 82.9 0.245 2.7
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 (All) 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 2DU8 2.9 50 29480 1578 96.93 0.21284 0.21284 0.21031 0.2094 0.25929 0.2566 RANDOM 33.748
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] -2.2 -0.18 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_3_deg 18.28 r_dihedral_angle_4_deg 16.974 r_dihedral_angle_1_deg 4.948 r_scangle_it 1.838 r_angle_refined_deg 1.347 r_mcangle_it 1.208 r_scbond_it 1.052 r_mcbond_it 0.67 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_3_deg 18.28 r_dihedral_angle_4_deg 16.974 r_dihedral_angle_1_deg 4.948 r_scangle_it 1.838 r_angle_refined_deg 1.347 r_mcangle_it 1.208 r_scbond_it 1.052 r_mcbond_it 0.67 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.277 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.08 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 134 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing