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Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 288 0.2 M ammonium acetate
12.5% (w/v) polyethylene glycol 4000
10% (v/v) glycerol
0.1 M sodium citrate, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.493 α = 90 b = 182.783 β = 90 c = 51.039 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 PIXEL DECTRIS PILATUS3 S 6M 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.25 48.3 99.9 0.061 0.066 0.026 1 21.3 6.6 67535 44.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.3 100 0.92 1.002 0.392 0.811 2.2 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2du8 2.25 48.3 1.97 67432 3329 99.89 0.1917 0.1887 0.2485 0.2266 random 46.77
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.5831 f_angle_d 1.1634 f_chiral_restr 0.1123 f_bond_d 0.0088 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10899 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 190
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing