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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 1LF5 pdb entry 1LF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 30% PEG8000, 0.1 M MES, 0.2 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.055 α = 90 b = 93.055 β = 90 c = 37.202 γ = 120
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 2011-02-10 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 2 50 99.5 0.113 10.2 4.7 12685 12614 -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 2 2.03 99.7 0.28 4.1 2.8
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 pdb entry 1LF5 2 50 12685 11632 596 96.48 0.23157 0.22934 0.2288 0.27436 0.2717 RANDOM 20.261
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] -0.17 -0.09 -0.17 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.708 r_dihedral_angle_4_deg 22.625 r_dihedral_angle_3_deg 17.125 r_dihedral_angle_1_deg 7.145 r_scangle_it 5.171 r_scbond_it 3.481 r_mcangle_it 2.248 r_angle_refined_deg 2.024 r_mcbond_it 1.261 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.708 r_dihedral_angle_4_deg 22.625 r_dihedral_angle_3_deg 17.125 r_dihedral_angle_1_deg 7.145 r_scangle_it 5.171 r_scbond_it 3.481 r_mcangle_it 2.248 r_angle_refined_deg 2.024 r_mcbond_it 1.261 r_chiral_restr 0.139 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 1323 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 43
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling