2YGN

WIF domain of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D3JPDB ENTRY 2D3J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PEG 8000 30 % W/V, 200 MM SODIUM ACETATE, 100 MM SODIUM CACODYLATE PH 6.5 .
Crystal Properties
Matthews coefficientSolvent content
2.8757

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.912α = 90
b = 134.138β = 90
c = 60.378γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.853098.80.116.35.317655
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)
11.851.9391.30.71.43.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 2D3J1.8527.5291640782892.480.2050.20390.2239
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]
18.7533-13.9848-4.7685
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d21.154
f_angle_d2.224
f_chiral_restr0.141
f_bond_d0.015
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1151
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms68

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing