2WGJ

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


X-RAY DIFFRACTION

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