2XP2

Structure of the Human Anaplastic Lymphoma Kinase in Complex with Crizotinib (PF-02341066)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WGJPDB ENTRY 2WGJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5286CO-CRYSTALS OF ALK KINASE DOMAIN WITH PF-02341066 WERE OBTAINED AT 13 DEGREES C BY USING HANGING-DROP VAPOR-DIFFUSION. 0.5 MICROLITERS OF 1:3 MOLAR RATIO OF 14.9 MG/ML PROTEIN SOLUTION TO PF02341066 WAS MIXED WITH 0.5 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 7-10% (W/V) MEPEG 5K, 0.1M MES, PH6.0-6.5 AND 0.15M (NH4)2SO4.
Crystal Properties
Matthews coefficientSolvent content
1.9938.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.633α = 90
b = 57.086β = 90
c = 104.709γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC CCD2010-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
11.86104.7192.80.07165.724837218.8
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)
11.861.96640.3322.3

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 2WGJ1.936.76238211147950.2070.2070.252RANDOM37
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]
-4.18-6.5510.73
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_scangle_it3.61
c_mcangle_it2.5
c_scbond_it2.39
c_mcbond_it1.56
c_angle_deg0.8
c_improper_angle_d0.69
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_scangle_it3.61
c_mcangle_it2.5
c_scbond_it2.39
c_mcbond_it1.56
c_angle_deg0.8
c_improper_angle_d0.69
c_bond_d0.005
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 Atoms2262
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms30

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
CNSphasing