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Crystal structure of human KRAS G12A mutant in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2 mol L-1 sodium acetate, 0.1 mol L-1 Tris pH 8.5, 26% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.773 α = 90 b = 93.773 β = 90 c = 119.918 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 RAYONIX MX225HE 2016-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 28.12 99.9 0.082 0.082 0.09 0.038 0.998 10.8 5.7 43235 43235
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 100 0.873 0.033 0.037 0.016 0.729 5.6 6314
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 4I8G 1.7 27.07 40983 2251 99.91 0.1727 0.1709 0.1835 0.2067 0.2167 RANDOM 30.481
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] -0.79 -0.4 -0.79 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.264 r_dihedral_angle_4_deg 18.651 r_dihedral_angle_3_deg 12.143 r_dihedral_angle_1_deg 6.206 r_angle_refined_deg 1.615 r_angle_other_deg 0.793 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.264 r_dihedral_angle_4_deg 18.651 r_dihedral_angle_3_deg 12.143 r_dihedral_angle_1_deg 6.206 r_angle_refined_deg 1.615 r_angle_other_deg 0.793 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2722 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing