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Structure of c-Met with pyrimidone inhibitor 7
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 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.741 α = 90 b = 78.648 β = 90 c = 129.257 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 mirrors 2004-04-19 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 2.6 20 99.1 0.068 13.2 3.2 23893 23678 -3 -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) 2.6 2.69 96.7 0.311 2.6 2.8 2277
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1r1w 2.6 20 22763 22426 1216 98.52 0.24662 0.24662 0.24444 0.2353 0.28772 RANDOM 42.974
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] 2.25 -2.53 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_dihedral_angle_3_deg 15.728 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_1_deg 4.362 r_scangle_it 1.154 r_angle_refined_deg 1.08 r_mcangle_it 0.923 r_scbond_it 0.725 r_mcbond_it 0.512 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_dihedral_angle_3_deg 15.728 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_1_deg 4.362 r_scangle_it 1.154 r_angle_refined_deg 1.08 r_mcangle_it 0.923 r_scbond_it 0.725 r_mcbond_it 0.512 r_nbtor_refined 0.305 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.087 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4320 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 74
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling