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Crystal structure of KRAS G12D in complex with GDP and compound 14
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 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.475 α = 90 b = 62.392 β = 91.86 c = 72.132 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 2021-12-14 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 1.2 29.64 87.8 0.998 8.9 4 89215
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 1.2 1.23 0.805
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.2 29.64 88742 4376 85.6 0.1911 0.1904 0.2033 0.2074 RANDOM 14
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] 0.2859 -0.2022 -0.2952 0.0093
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.62 t_omega_torsion 4.08 t_angle_deg 0.97 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 291 Heterogen Atoms 152
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling BUSTER phasing