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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.
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 48.84
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 95 CCD ADSC CCD 2006-05-01 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 2.2 50 93.7 0.1 12.9 3.7 16974 16.6
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 2.2 2.25 71.6 0.43 1.98 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2.2 47.26 16855 505 93.7 0.204 0.1994 0.256 0.2479 RANDOM 34.6
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 -11.15 12.58
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 3.06 c_mcangle_it 2.16 c_scbond_it 2.15 c_mcbond_it 1.35 c_angle_deg 0.8 c_improper_angle_d 0.62 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.3 c_scangle_it 3.06 c_mcangle_it 2.16 c_scbond_it 2.15 c_mcbond_it 1.35 c_angle_deg 0.8 c_improper_angle_d 0.62 c_bond_d 0.006 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 Atoms Number Protein Atoms 2309 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 27
Software Software Software Name Purpose CNX refinement HKL-2000 data reduction SCALEPACK data scaling CCP4 phasing