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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 4.5 291 28% PEG8000, 0.1 M sodium acetate, 5% DMSO, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.92 36.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.132 α = 90 b = 41.473 β = 90 c = 91.726 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 2010-01-01 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 1.76 45.86 99.5 0.099 15.2 4.7 15410 15330 -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 1.76 1.79 93.8 0.106 6.8 2.1
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 1.76 45.86 15410 14433 756 98.75 0.15398 0.15149 0.1512 0.20096 0.2011 RANDOM 16.773
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] -1.17 1.4 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.82 r_dihedral_angle_4_deg 22.31 r_dihedral_angle_3_deg 13.897 r_dihedral_angle_1_deg 5.936 r_scangle_it 5.248 r_scbond_it 3.29 r_angle_refined_deg 2.057 r_mcangle_it 2.028 r_mcbond_it 1.218 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.82 r_dihedral_angle_4_deg 22.31 r_dihedral_angle_3_deg 13.897 r_dihedral_angle_1_deg 5.936 r_scangle_it 5.248 r_scbond_it 3.29 r_angle_refined_deg 2.057 r_mcangle_it 2.028 r_mcbond_it 1.218 r_chiral_restr 0.15 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 1358 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 47
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling