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Crystal structure of c-Met in complex with pyrazolone inhibitor 58a
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 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.113 α = 90 b = 82 β = 90 c = 127.008 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++ 2005-09-19 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 2.1 50 97.2 0.052 28.8 3.3 21582 -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 2.1 2.17 95.7 0.235 2.7 2096
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 2.1 50 21087 20461 1104 97.03 0.2084 0.2058 0.2011 0.2572 0.2539 RANDOM 30.7897
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] 1.56 -2.1 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.165 r_dihedral_angle_4_deg 15.943 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 4.434 r_scangle_it 1.77 r_mcangle_it 1.184 r_scbond_it 1.091 r_angle_refined_deg 1.09 r_mcbond_it 0.668 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.165 r_dihedral_angle_4_deg 15.943 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 4.434 r_scangle_it 1.77 r_mcangle_it 1.184 r_scbond_it 1.091 r_angle_refined_deg 1.09 r_mcbond_it 0.668 r_nbtor_refined 0.302 r_nbd_refined 0.169 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 40
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection DENZO data reduction AMoRE phasing