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Crystal structure of KRAS-G12D/G75A mutant, GDP-bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5US4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.2 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.133 α = 90 b = 85.133 β = 90 c = 41.929 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 PIXEL DECTRIS EIGER X 16M 2022-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2 73.73 99.7 0.11599999999999999 0.129 0.991 8.52 5.13 22917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.997 1.11 0.41700000000000004
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 2.03 73.73 20732 1102 99.34 0.16117 0.15997 0.165 0.18261 0.1817 RANDOM 40.642
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] -6.06 -6.06 12.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.674 r_dihedral_angle_2_deg 12.63 r_long_range_B_refined 7.84 r_dihedral_angle_1_deg 6.607 r_mcangle_it 4.249 r_scbond_it 2.859 r_mcbond_it 2.826 r_angle_refined_deg 1.2 r_chiral_restr 0.091 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.674 r_dihedral_angle_2_deg 12.63 r_long_range_B_refined 7.84 r_dihedral_angle_1_deg 6.607 r_mcangle_it 4.249 r_scbond_it 2.859 r_mcbond_it 2.826 r_angle_refined_deg 1.2 r_chiral_restr 0.091 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2585 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing