4QFD | pdb_00004qfd

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4289DAAO 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 coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.49α = 90
b = 86.49β = 90
c = 187.97γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.12709SSRLBL7-1

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
12.855099.10.06921.766.619576-369.55
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)
12.852.9299.80.7283.27.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3CUK2.8519.9119539100099.130.250.2480.250.2870.29RANDOM85.56
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]
1.631.631.63-5.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.746
r_dihedral_angle_3_deg15.539
r_dihedral_angle_4_deg12.668
r_dihedral_angle_1_deg5.687
r_mcangle_it1.849
r_angle_refined_deg1.104
r_mcbond_other1.067
r_mcbond_it1.066
r_angle_other_deg0.751
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.746
r_dihedral_angle_3_deg15.539
r_dihedral_angle_4_deg12.668
r_dihedral_angle_1_deg5.687
r_mcangle_it1.849
r_angle_refined_deg1.104
r_mcbond_other1.067
r_mcbond_it1.066
r_angle_other_deg0.751
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms4885
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms154

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction