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Co-crystal structure of compound 2 (3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid) and FAD bound to human DAAO at 2.85A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CUK pdb entry 3CUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 289 DAAO AT 2 MG/ML IN 50 MM SODIUM PHOSPHATE PH 6.6, 10 UM FAD INCUBATED WITH 5-FOLD EXCESS OF SEP-0374036 OVERNIGHT AT 277 K, CRYSTALLIZED AGAINST 13.6% PEG3350, 0.1 M TRIS PH 7.4, 150 MM POTASSIUM CITRATE TRIBASIC AND 20 MM GLYCEROL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 241709B5, UNIQUE PUCK ID XSS6-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.49 α = 90 b = 86.49 β = 90 c = 187.97 γ = 120
Symmetry Space Group P 32 2 1
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 315r 2013-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1
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 2.85 50 99.1 0.069 21.76 6.6 19576 -3 69.55
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 2.85 2.92 99.8 0.728 3.2 7.2
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 3CUK 2.85 19.91 19539 1000 99.13 0.25 0.248 0.2462 0.287 0.2858 RANDOM 85.56
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] 1.63 1.63 1.63 -5.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.746 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_4_deg 12.668 r_dihedral_angle_1_deg 5.687 r_mcangle_it 1.849 r_angle_refined_deg 1.104 r_mcbond_other 1.067 r_mcbond_it 1.066 r_angle_other_deg 0.751 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.746 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_4_deg 12.668 r_dihedral_angle_1_deg 5.687 r_mcangle_it 1.849 r_angle_refined_deg 1.104 r_mcbond_other 1.067 r_mcbond_it 1.066 r_angle_other_deg 0.751 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4885 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 154
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction