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GDP-bound KRAS G12D in complex with MCB-294
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M Tris, pH 8.5, 26% (w/v) PEG 3350, 0.2 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.037 α = 90 b = 95.037 β = 90 c = 121.012 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 RIGAKU HyPix-Arc 150 2025-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
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 1.8 68.06 99.8 1 56.7 14.7 19663
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 1.8 1.87 0.989
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 1.8 17.02 18461 936 98.44 0.17619 0.17447 0.21051 0.2006 RANDOM 15.572
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] -0.19 -0.1 -0.19 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.306 r_dihedral_angle_4_deg 20.698 r_dihedral_angle_3_deg 12.779 r_dihedral_angle_1_deg 6.062 r_long_range_B_refined 5.224 r_long_range_B_other 5.224 r_scangle_other 3.866 r_scbond_it 2.518 r_scbond_other 2.516 r_mcangle_it 2.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.306 r_dihedral_angle_4_deg 20.698 r_dihedral_angle_3_deg 12.779 r_dihedral_angle_1_deg 6.062 r_long_range_B_refined 5.224 r_long_range_B_other 5.224 r_scangle_other 3.866 r_scbond_it 2.518 r_scbond_other 2.516 r_mcangle_it 2.432 r_mcangle_other 2.431 r_angle_refined_deg 1.995 r_angle_other_deg 1.787 r_mcbond_it 1.674 r_mcbond_other 1.656 r_chiral_restr 0.093 r_gen_planes_refined 0.016 r_bond_refined_d 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1359 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SAINT data scaling PHASER phasing REFMAC refinement