3ZXZ

X-ray Structure of PF-04217903 bound to the kinase domain of c-Met


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6286CRYSTALS WERE OBTAINED AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD USING 1.2 MICROLITERS OF PROTEIN SOLUTION (CONTAINING 7-13 MG/ML C-MET KD PLUS A 5 FOLD MOLAR EXCESS OF PF-04217903) AND 1.2 MICROLITERS OF MOTHER LIQUOR SOLUTION (0.05 M CITRATE-PHOSHPHATE 4.6, 0-0.275 M NACL, AND 21% W/V PEG 3350).
Crystal Properties
Matthews coefficientSolvent content
2.3948.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.74α = 90
b = 94.125β = 90
c = 46.138γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray87CCDADSC CCD2006-10-06MSINGLE 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
11.85085.30.0811.14.227447213.2
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)
11.81.8637.20.253.272.5

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 2WGJ1.841.432632078282.90.1850.1850.221RANDOM29.1
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]
-3.23-9.7412.97
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.3
c_scangle_it3.18
c_scbond_it2.16
c_mcangle_it1.84
c_mcbond_it1.24
c_angle_deg0.8
c_improper_angle_d0.59
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.3
c_scangle_it3.18
c_scbond_it2.16
c_mcangle_it1.84
c_mcbond_it1.24
c_angle_deg0.8
c_improper_angle_d0.59
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 Atoms2309
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms28

Software

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