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Co-crystal structure of compound 3 (4-hydroxy-6-[2-(7-hydroxy-2-oxo-4-phenyl-2h-chromen-6-yl)ethyl]pyridazin-3(2h)-one) and FAD bound to human DAAO at 2.4A
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 6.6 289 protein at 2 mg/mL in 50mM sodium phosphate pH 6.6, 10uM FAD against 30%PEG2000MME, 0.1M POTASSIUM THIOCYANATE supplemented with 20% ethylene glycol as cryo-protectant, unique crystal ID 246094_h11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.39 α = 90 b = 60.93 β = 90 c = 258.45 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD 2013-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.4 50 99.6 0.096 12.25 28446 -3 40.26
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 2.4 2.46 99.9 0.486 3.2
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 2.4 43.79 28410 1437 0.179 0.176 0.1806 0.227 0.2288 RANDOM 33.06
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] -0.24 0.53 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 13.864 r_dihedral_angle_1_deg 6.793 r_mcangle_it 3.126 r_mcbond_it 1.952 r_mcbond_other 1.951 r_angle_refined_deg 1.595 r_angle_other_deg 0.819 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 13.864 r_dihedral_angle_1_deg 6.793 r_mcangle_it 3.126 r_mcbond_it 1.952 r_mcbond_other 1.951 r_angle_refined_deg 1.595 r_angle_other_deg 0.819 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5103 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 163
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction