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X-ray structure of c-Met with triazolopyridazine inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 298 0.1M HEPES pH 7.8, 15% PEG 4K, 6% 2-Propanol, 40mM BME, and 3% Ethanol., VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.058 α = 90 b = 43.44 β = 90 c = 157.827 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 130 IMAGE PLATE RIGAKU RAXIS IV++ varimax optics 2006-04-04 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 1.9 50 92.1 0.05 28 3 23768 21891 -1 -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) 1.9 1.97 81.9 0.17 6.5 2.2 1894
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2RFN 1.9 50 22451 20714 1089 92.26 0.2379 0.2379 0.23603 0.2296 0.27545 0.2645 RANDOM 29.952
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] 0.42 0.76 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.456 r_dihedral_angle_4_deg 14.232 r_dihedral_angle_3_deg 12.841 r_dihedral_angle_1_deg 4.878 r_scangle_it 1.676 r_scbond_it 1.144 r_angle_refined_deg 1.057 r_mcangle_it 0.999 r_mcbond_it 0.601 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.456 r_dihedral_angle_4_deg 14.232 r_dihedral_angle_3_deg 12.841 r_dihedral_angle_1_deg 4.878 r_scangle_it 1.676 r_scbond_it 1.144 r_angle_refined_deg 1.057 r_mcangle_it 0.999 r_mcbond_it 0.601 r_nbtor_refined 0.302 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2149 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing