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Crystal Structure of small molecule ARS-107 covalently bound to K-Ras G12C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 29% PEG 4000, 0.2 M CaCl2, 0.1 M Tris pH=8.5
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.14 α = 77 b = 39.88 β = 81.24 c = 62.43 γ = 77.58
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 ADSC QUANTUM 315r 2013-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.999995 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.29 32.171 90.4 0.085 0.104 0.059 6.1 2.8 68823
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.36 87.5 0.341 0.341 0.415 0.234 2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5F2E 1.29 32.171 65427 3371 90.39 0.1841 0.1824 0.1918 0.2183 0.2231 RANDOM 15.999
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] 0.06 -0.38 0.38 0.92 1.08 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.079 r_dihedral_angle_3_deg 13.735 r_dihedral_angle_4_deg 13.681 r_dihedral_angle_1_deg 5.84 r_angle_refined_deg 2.478 r_angle_other_deg 2.199 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.015 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.079 r_dihedral_angle_3_deg 13.735 r_dihedral_angle_4_deg 13.681 r_dihedral_angle_1_deg 5.84 r_angle_refined_deg 2.478 r_angle_other_deg 2.199 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2642 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 114
Software Software Software Name Purpose iMOSFLM data collection SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction