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Crystal structure of c-Met in complex with pyrazolone inhibitor 26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFN pdb entry 2RFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 293 12% PEG 6000, 1.0 M lithium chloride, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.61 α = 90 b = 81.97 β = 90 c = 127.038 γ = 90
Symmetry Space Group C 2 2 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++ 2005-02-07 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 20 91.8 0.054 41.6 4.97 116897 23515 -3
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 2 2.07 57.5 0.26 1434
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 (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 2RFN 2 19.71 23067 21192 2314 91.87 0.2207 0.2149 0.2103 0.2737 0.2674 RANDOM 31.4478
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] 1.76 -2.95 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_4_deg 12.595 r_dihedral_angle_1_deg 4.717 r_scangle_it 1.959 r_mcangle_it 1.277 r_scbond_it 1.217 r_angle_refined_deg 1.202 r_mcbond_it 0.727 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_4_deg 12.595 r_dihedral_angle_1_deg 4.717 r_scangle_it 1.959 r_mcangle_it 1.277 r_scbond_it 1.217 r_angle_refined_deg 1.202 r_mcbond_it 0.727 r_nbtor_refined 0.3 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 39
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection AMoRE phasing