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Crystal structure of KRAS G12D in complex with GDP and compound 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286.15 0.1 M Sodium Acetate pH 4.5, 40% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.815 α = 90 b = 62.166 β = 91.86 c = 71.925 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS EIGER X 9M 2021-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 29.77 84 0.999 11.5 3.3 59639
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 0.745
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.35 29.77 58543 2926 80.1 0.1895 0.1882 0.1838 0.2148 0.2062 RANDOM 14.65
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] 0.6341 0.4063 -0.0637 -0.5705
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.57 t_omega_torsion 3.79 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 144
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling BUSTER phasing