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Structure of c-Met with pyrimidone inhibitor 50
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 2.73 55.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.205 α = 90 b = 78.25 β = 90 c = 129.684 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 2004-07-30 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 2.2 19.64 97.8 0.057 20 3.6 40217 39332 -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) 2.2 2.28 93.9 0.422 2.5 3699
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 2.2 19.64 38087 37276 1967 97.87 0.25746 0.25746 0.25565 0.2483 0.29185 RANDOM 38.372
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] 2.33 -1.59 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_3_deg 15.583 r_dihedral_angle_4_deg 13.805 r_dihedral_angle_1_deg 4.773 r_scangle_it 1.493 r_angle_refined_deg 1.096 r_scbond_it 0.924 r_mcangle_it 0.915 r_mcbond_it 0.51 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_3_deg 15.583 r_dihedral_angle_4_deg 13.805 r_dihedral_angle_1_deg 4.773 r_scangle_it 1.493 r_angle_refined_deg 1.096 r_scbond_it 0.924 r_mcangle_it 0.915 r_mcbond_it 0.51 r_nbtor_refined 0.303 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4299 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 76
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling