4QFC

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CUKpdb entry 3CUK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.6289protein 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 coefficientSolvent content
2.2846.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.39α = 90
b = 60.93β = 90
c = 258.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.45099.60.09612.2528446-340.26
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4699.90.4863.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3CUK2.443.792841014370.1790.1760.227RANDOM33.06
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]
-0.240.53-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.841
r_dihedral_angle_4_deg17.5
r_dihedral_angle_3_deg13.864
r_dihedral_angle_1_deg6.793
r_mcangle_it3.126
r_mcbond_it1.952
r_mcbond_other1.951
r_angle_refined_deg1.595
r_angle_other_deg0.819
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.841
r_dihedral_angle_4_deg17.5
r_dihedral_angle_3_deg13.864
r_dihedral_angle_1_deg6.793
r_mcangle_it3.126
r_mcbond_it1.952
r_mcbond_other1.951
r_angle_refined_deg1.595
r_angle_other_deg0.819
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5103
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms163

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction