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x-ray structure of c-Met with inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R1W PDB entry 1R1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 298 12% PEG 6000, 1.0M LiCl2, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.509 α = 90 b = 78.919 β = 90 c = 129.128 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++ osmic 2004-08-20 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 2.5 20 97.5 0.073 20.5 25637 24997 -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 2.5 2.59 95.4 0.403 2.8
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-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 1R1W 2.5 20 24997 1305 97.6 0.24061 0.24061 0.23788 0.2312 0.29414 0.2825 RANDOM 51.24
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] 4.68 -3.39 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.518 r_dihedral_angle_3_deg 17.748 r_dihedral_angle_4_deg 17.166 r_dihedral_angle_1_deg 5.352 r_scangle_it 1.369 r_angle_refined_deg 1.254 r_scbond_it 0.856 r_mcangle_it 0.751 r_mcbond_it 0.423 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.518 r_dihedral_angle_3_deg 17.748 r_dihedral_angle_4_deg 17.166 r_dihedral_angle_1_deg 5.352 r_scangle_it 1.369 r_angle_refined_deg 1.254 r_scbond_it 0.856 r_mcangle_it 0.751 r_mcbond_it 0.423 r_nbtor_refined 0.312 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.096 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4233 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing