5VC5

Crystal structure of human WEE1 kinase domain in complex with PD-166285


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V5Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92919.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM PD-166285
Crystal Properties
Matthews coefficientSolvent content
2.1141.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.53α = 90
b = 44.4β = 99.97
c = 61.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.9335.90798.40.0280.034125.072.73620256-328.08
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.9899.20.310.380.9063.652.72

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5V5Y1.9335.9071.3620255101398.440.17630.216947.1873
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.78
f_angle_d1.368
f_chiral_restr0.057
f_bond_d0.012
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2077
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms91

Software

Software
Software NamePurpose
XSCALEdata scaling
SERGUIdata collection
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing