☰ Navigation Tabs
CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THE HEPATOCYTE GROWTH FACTOR RECEPTOR C-MET IN COMPLEX WITH ALTIRATINIB ANALOG DP-4157
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G15 PDB entry 2g15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Protein at 9.5mg/ml in 20 mM Tris pH 8.5, 100mM NaCl, 14mM 2-mercaptoethanol with 5-molar excess of compound; crystallization condition: 1.0M diammonium hydrogen phosphate, 0.2M sodium chloride, 0.1M citrate pH 5.0 and 7.5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.69 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.13 α = 90 b = 115.88 β = 92.92 c = 90.16 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2009-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9999 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 20 98.3 0.1 0.12 11.36 3.2 23076 -3 47.861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.78 99.3 0.689 0.827 1.97 3.2
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 2g15 2.6 19.65 21913 1161 98.25 0.2057 0.2036 0.2081 0.2449 0.2494 RANDOM 43.412
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] -1.37 -0.51 -3.3 4.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.051 r_dihedral_angle_4_deg 19.521 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_1_deg 5.515 r_mcangle_it 3.823 r_mcbond_it 2.258 r_mcbond_other 2.255 r_angle_refined_deg 1.196 r_angle_other_deg 0.893 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.051 r_dihedral_angle_4_deg 19.521 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_1_deg 5.515 r_mcangle_it 3.823 r_mcbond_it 2.258 r_mcbond_other 2.255 r_angle_refined_deg 1.196 r_angle_other_deg 0.893 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4603 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 74
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building REFMAC refinement