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Crystal structure of c-Met with triazolopyridazine inhibitor 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CD8 PDB entry 3CD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 298 15% PEG 4000, 0.1 M HEPES, 40 mM beta-mercaptoethanol, 6% isopropanol, 3% ethanol
, pH 7.8, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.977 α = 90 b = 43.241 β = 90 c = 158.232 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 IMAGE PLATE RIGAKU RAXIS IV++ varimax optics 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 41.7 97.5 0.043 29.2 3.4 20349 19840 30.6
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) 2 2.07 93.3 0.174 7.1 2.8 1976
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 (All) 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 3CD8 2 41.7 19800 1007 97.77 0.227 0.225 0.221 0.267 0.2594 RANDOM 32.707
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] -0.46 2.06 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.499 r_dihedral_angle_4_deg 18.571 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_1_deg 4.964 r_scangle_it 1.315 r_mcangle_it 1.216 r_angle_refined_deg 1.025 r_scbond_it 0.892 r_mcbond_it 0.718 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.499 r_dihedral_angle_4_deg 18.571 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_1_deg 4.964 r_scangle_it 1.315 r_mcangle_it 1.216 r_angle_refined_deg 1.025 r_scbond_it 0.892 r_mcbond_it 0.718 r_nbtor_refined 0.302 r_nbd_refined 0.171 r_symmetry_vdw_refined 0.127 r_xyhbond_nbd_refined 0.104 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2244 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 29
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection DENZO data reduction AMoRE phasing