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Structure of the kinase domain of c-Met bound to XL880 (GSK1363089)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house c-Met complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 12% PEG 4000, 15% isopropanol, 25 mM MOPS, pH 6.5, 150 mM NaCl, 2 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.925 α = 90 b = 43.017 β = 91.61 c = 89.618 γ = 90
Symmetry Space Group P 1 21 1
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 HTC 2004-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.02 35.27 100 0.047 0.047 18.6 3.1 19225 19220 25.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.02 2.13 99.9 0.268 0.268 3.8 3 2788
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 in house c-Met complex 2.02 35.27 19211 18228 983 99.92 0.19368 0.19064 0.1872 0.25164 0.255 RANDOM 25.868
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] -0.58 -0.25 1.04 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.933 r_dihedral_angle_4_deg 21.086 r_dihedral_angle_3_deg 12.878 r_dihedral_angle_1_deg 6.447 r_scangle_it 3.657 r_scbond_it 2.587 r_angle_refined_deg 2.361 r_mcangle_it 1.922 r_mcbond_it 1.199 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.933 r_dihedral_angle_4_deg 21.086 r_dihedral_angle_3_deg 12.878 r_dihedral_angle_1_deg 6.447 r_scangle_it 3.657 r_scbond_it 2.587 r_angle_refined_deg 2.361 r_mcangle_it 1.922 r_mcbond_it 1.199 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.282 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.187 r_symmetry_vdw_refined 0.164 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2216 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 46
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling