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X-ray Structure of c-Met kinase in complex with inhibitor (S)-3-(1-(1H-pyrrolo(2,3-b)pyridin-3-yl)ethyl)-N-isopropyl-(1,2,4)triazolo(4,3- b)pyridazin-6-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WGJ PDB ENTRY 2WGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 286 C-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 coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.997 α = 90 b = 94.509 β = 90 c = 46.834 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 97 CCD ADSC QUANTUM 315 2007-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 50 87.5 0.07 32 3.8 58868 14.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 53.1 0.34 2 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WGJ 1.4 41.46 58519 55089 2794 82.4 0.194 0.193 0.2534 0.211 0.2597 RANDOM 25.4
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] -3.46 -6.56 10.02
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 2.94 c_scbond_it 2.14 c_mcangle_it 1.81 c_mcbond_it 1.13 c_angle_deg 0.8 c_improper_angle_d 0.63 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 2.94 c_scbond_it 2.14 c_mcangle_it 1.81 c_mcbond_it 1.13 c_angle_deg 0.8 c_improper_angle_d 0.63 c_bond_d 0.004 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 Atoms Number Protein Atoms 2310 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 24
Software Software Software Name Purpose CNX refinement HKL-2000 data reduction SCALEPACK data scaling CNX phasing