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Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-mediated Activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 32% PEG1500, 0.7% 1-Butanol, pH 6.1-8.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.95 36.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.219 α = 90 b = 41.924 β = 90 c = 91.448 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 100 CCD Bruker Platinum 135 2010-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 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 1.7 45.72 94.4 0.106 8.6 17334 16370 -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 1.7 1.73 83.8 0.151 4.3 1.8
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 4EPV 1.7 45.72 17334 15325 810 93.31 0.1883 0.18565 0.185 0.24 0.2418 RANDOM 17.211
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] -0.84 1.29 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.962 r_dihedral_angle_4_deg 21.373 r_dihedral_angle_3_deg 14.616 r_dihedral_angle_1_deg 6.017 r_scangle_it 4.826 r_scbond_it 3.148 r_angle_refined_deg 2.078 r_mcangle_it 1.986 r_mcbond_it 1.272 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.962 r_dihedral_angle_4_deg 21.373 r_dihedral_angle_3_deg 14.616 r_dihedral_angle_1_deg 6.017 r_scangle_it 4.826 r_scbond_it 3.148 r_angle_refined_deg 2.078 r_mcangle_it 1.986 r_mcbond_it 1.272 r_chiral_restr 0.132 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1355 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 47
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling