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Crystal structure of human D-amino acid oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AN9 PDB ENTRY 1AN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 288 10% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, 12% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.976 α = 90 b = 183.184 β = 90 c = 51.075 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 CCD ADSC QUANTUM 315 2006-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.5 116.25 99.5 0.077 13.4 5.8 49644
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) 2.5 2.59 99.8 0.377 5.5
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 (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 2.5 46.78 47032 2516 99.08 0.22535 0.22296 0.2234 0.27006 0.2189 RANDOM 51.856
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] 3.37 -1.64 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.564 r_dihedral_angle_4_deg 17.747 r_dihedral_angle_3_deg 17.464 r_angle_other_deg 13.385 r_dihedral_angle_1_deg 5.14 r_scangle_it 3.039 r_scbond_it 2.215 r_mcangle_it 1.552 r_angle_refined_deg 1.384 r_mcbond_it 1.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.564 r_dihedral_angle_4_deg 17.747 r_dihedral_angle_3_deg 17.464 r_angle_other_deg 13.385 r_dihedral_angle_1_deg 5.14 r_scangle_it 3.039 r_scbond_it 2.215 r_mcangle_it 1.552 r_angle_refined_deg 1.384 r_mcbond_it 1.052 r_nbtor_refined 0.313 r_nbtor_other 0.29 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.144 r_mcbond_other 0.136 r_bond_other_d 0.105 r_chiral_restr 0.083 r_gen_planes_other 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_nbd_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_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 256 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing