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Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2 uL + 0.2 uL drops containing 40 mg/mL KRas, 0.1 M TrisCl, 25% polyethylene glycol 4000, 0.2 M NaOAc, 2% benzamidine-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.374 α = 90 b = 79.374 β = 90 c = 77.749 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 93 CCD MARMOSAIC 325 mm CCD Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs 2009-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 30 98.7 0.059 18.1 5.3 14782 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.99 82.2 0.158 7.4 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 25.92 15563 14782 781 99.84 0.17211 0.17022 0.1782 0.20705 0.1775 RANDOM 39.076
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] -0.41 -0.2 -0.41 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.387 r_dihedral_angle_4_deg 20.783 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_1_deg 7.5 r_scangle_it 2.88 r_scbond_it 2.084 r_angle_refined_deg 2.066 r_mcangle_it 1.358 r_mcbond_it 1.2 r_angle_other_deg 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.387 r_dihedral_angle_4_deg 20.783 r_dihedral_angle_3_deg 14.615 r_dihedral_angle_1_deg 7.5 r_scangle_it 2.88 r_scbond_it 2.084 r_angle_refined_deg 2.066 r_mcangle_it 1.358 r_mcbond_it 1.2 r_angle_other_deg 0.953 r_symmetry_hbond_refined 0.498 r_symmetry_vdw_other 0.308 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.227 r_nbd_other 0.214 r_mcbond_other 0.211 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.178 r_metal_ion_refined 0.105 r_chiral_restr 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1417 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 48
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling