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Crystal structure of C-MET kinase domain in complex with N'-((3Z)-4- chloro-7-methyl-2-oxo-1,2-dihydro-3H-indol-3-ylidene)-2-(4- hydroxyphenyl)propanohydrazide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WKM PDB ENTRY 2WKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 286 CRYSTALS 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 THE C-MET INHIBITOR COMPOUND) 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 coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.864 α = 90 b = 94.373 β = 90 c = 45.766 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 87 CCD ADSC CCD 2011-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 1.74 50 67.2 0.12 17 6 28793 1 10.1
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 1.87 1.96 67.2 0.36 1 4.8
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-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 2WKM 1.87 47.19 24712 723 87.4 0.196 0.196 0.1921 0.226 0.2259 RANDOM 24.1
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] -7.08 -5.09 12.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 3.19 c_scbond_it 2.26 c_mcangle_it 1.84 c_mcbond_it 1.23 c_angle_deg 0.8 c_improper_angle_d 0.6 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 3.19 c_scbond_it 2.26 c_mcangle_it 1.84 c_mcbond_it 1.23 c_angle_deg 0.8 c_improper_angle_d 0.6 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 2284 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 25
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNX phasing