6CZ4

Structure of the PTK6 kinase domain bound to a type II inhibitor 2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-5-(1-methyl-1H-imidazol-4-yl)pyridine-3-carboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2861.25 M Sodium dihydrogen phosphate, 0.89 M di-Potassium hydrogen phosphate, 0.2 M Lithium sulfate, 0.1 M CHES, pH 9.8, 13o C
Crystal Properties
Matthews coefficientSolvent content
2.3146.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.914α = 90
b = 54.873β = 90
c = 134.629γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.4850.8297.90.0370.0410.0160.99922.95.94682024.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.5686.80.4180.4850.2390.9032.63.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.550.8245221220298.40.2030.2030.209RANDOM28.7
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]
-0.76.45-5.75
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.3
c_scangle_it3.32
c_scbond_it2.16
c_mcangle_it2.14
c_mcbond_it1.32
c_angle_deg0.8
c_improper_angle_d0.61
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.3
c_scangle_it3.32
c_scbond_it2.16
c_mcangle_it2.14
c_mcbond_it1.32
c_angle_deg0.8
c_improper_angle_d0.61
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2109
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms37

Software

Software
Software NamePurpose
CNXrefinement
XDSdata reduction
Aimlessdata scaling
CNXphasing