2WGJ

X-ray Structure of PF-02341066 bound to the kinase domain of c-Met


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LCKPDB ENTRY 3LCK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6286CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 13 DEGREES CELCIUS. 1-2 MICROLITERS OF PROTEIN SOLUTION AT 7-15 MG/ML WAS MIXEDWITH AN EQUAL VOLUME OF PRECIPITATING SOLUTION (0-275 MM SODIUM CHLORIDE, 21% (W/V PEG 3350, 50 MM CITRATE-PHOSPHATE PH 4.6)
Crystal Properties
Matthews coefficientSolvent content
2.3647.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.926α = 90
b = 94.192β = 90
c = 45.99γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC CCDPINHOLE COLLIMATOR2006-04-30MSINGLE 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
125078.10.06203.9181921
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)
122.0538.50.292.52.8

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 3LCK219.961719592678.050.214850.213960.23153RANDOM40.859
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]
-2.06-4.326.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.148
r_scangle_it2.347
r_scbond_it1.386
r_mcangle_it1.086
r_angle_refined_deg1.081
r_mcbond_it0.572
r_symmetry_hbond_refined0.213
r_nbd_refined0.193
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.148
r_scangle_it2.347
r_scbond_it1.386
r_mcangle_it1.086
r_angle_refined_deg1.081
r_mcbond_it0.572
r_symmetry_hbond_refined0.213
r_nbd_refined0.193
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.141
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2309
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing