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Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met in complex with the microbial alkaloid K-252a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 277 PEG 5000 MME, isopropanol, Hepes, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.969 α = 90 b = 46.247 β = 90 c = 158.379 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2002-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.8 30 96 0.043 34 3.45 29021
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) 1.8 1.86 89.2 0.079 12.2 2638
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 30 29021 27531 1436 96.03 0.17093 0.16959 0.19726 RANDOM 12.236
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] 0.43 -0.19 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.493 r_scangle_it 3.186 r_scbond_it 1.968 r_angle_refined_deg 1.81 r_mcangle_it 1.305 r_angle_other_deg 0.821 r_mcbond_it 0.671 r_symmetry_vdw_other 0.328 r_xyhbond_nbd_refined 0.299 r_nbd_refined 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.493 r_scangle_it 3.186 r_scbond_it 1.968 r_angle_refined_deg 1.81 r_mcangle_it 1.305 r_angle_other_deg 0.821 r_mcbond_it 0.671 r_symmetry_vdw_other 0.328 r_xyhbond_nbd_refined 0.299 r_nbd_refined 0.249 r_nbd_other 0.24 r_symmetry_vdw_refined 0.22 r_symmetry_hbond_refined 0.166 r_nbtor_other 0.081 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2397 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement ProDC data collection SCALEPACK data scaling EPMR phasing