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Crystal Structure of Human D-Amino Acid Oxidase in Complex with Imino-Serine
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 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.661 α = 90 b = 181.745 β = 90 c = 50.717 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 2006-11-09 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 3.2 50 97.5 0.133 7.2 3.7 23223
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 3.2 3.31 92.3 0.223 3.4
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 3.2 50 21972 1187 97.23 0.22396 0.22396 0.22111 0.2194 0.2756 0.2735 RANDOM 40.757
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] 3.96 -6.9 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.678 r_dihedral_angle_3_deg 19.143 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_1_deg 4.843 r_scangle_it 1.921 r_angle_refined_deg 1.506 r_scbond_it 1.413 r_mcangle_it 1.136 r_mcbond_it 0.719 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.678 r_dihedral_angle_3_deg 19.143 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_1_deg 4.843 r_scangle_it 1.921 r_angle_refined_deg 1.506 r_scbond_it 1.413 r_mcangle_it 1.136 r_mcbond_it 0.719 r_nbtor_refined 0.319 r_nbd_refined 0.255 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.11 r_bond_refined_d 0.014 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 112 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing