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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 4EPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 291 25% PEG1500, 0.1 M MMT, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.91 35.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.14 α = 90 b = 41.066 β = 90 c = 91.955 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 2010-01-15 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 1.35 45.98 96.9 0.092 14.2 4.1 33312 32293 -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 1.35 1.37 72.4 0.2 4.1 2.2
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 4EPT 1.35 45.98 33312 30436 1621 96.34 0.16544 0.16393 0.1624 0.19385 0.1928 RANDOM 13.884
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] -0.35 0.51 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.267 r_dihedral_angle_4_deg 19.952 r_dihedral_angle_3_deg 11.66 r_dihedral_angle_1_deg 5.613 r_scangle_it 4.82 r_scbond_it 3.119 r_angle_refined_deg 2.354 r_mcangle_it 2.11 r_mcbond_it 1.295 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.267 r_dihedral_angle_4_deg 19.952 r_dihedral_angle_3_deg 11.66 r_dihedral_angle_1_deg 5.613 r_scangle_it 4.82 r_scbond_it 3.119 r_angle_refined_deg 2.354 r_mcangle_it 2.11 r_mcbond_it 1.295 r_chiral_restr 0.158 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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 236 Heterogen Atoms 48
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling