3ZC5

X-ray Structure of c-Met kinase in complex with inhibitor (S)-6-(1-(6- (1-methyl-1H-pyrazol-4-yl)-(1,2,4)triazolo(4,3-b)pyridazin-3-yl)ethyl) quinoline.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6286C-MET COCRYSTALS WERE OBTAINED AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1.2 MICROL OF PROTEIN SOLUTION (CONTAINING 7-13 MG/ML C-MET KD (RESIDUES 1051-1348) WITH A 5 FOLD MOLAR EXCESS OF SELECTED C-MET INHIBITOR) WITH 1.2 MICROL OF SOLUTION CONTAINING (0.05 M CITRATE-PHOSPHATE PH 4.6, 0-0.275 M NACL, AND 17-21% POLYETHYLENE GLYCOL MW=3350).
Crystal Properties
Matthews coefficientSolvent content
2.448.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.997α = 90
b = 94.509β = 90
c = 46.834γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC CCD2006-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

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
12.25093.70.112.93.71697416.6
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)
12.22.2571.60.431.982.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WGJ2.247.261685550593.70.2040.256RANDOM34.6
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]
-1.43-11.1512.58
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.3
c_scangle_it3.06
c_mcangle_it2.16
c_scbond_it2.15
c_mcbond_it1.35
c_angle_deg0.8
c_improper_angle_d0.62
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.3
c_scangle_it3.06
c_mcangle_it2.16
c_scbond_it2.15
c_mcbond_it1.35
c_angle_deg0.8
c_improper_angle_d0.62
c_bond_d0.006
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 Atoms2309
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms27

Software

Software
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing