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GppNHp-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 0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 26% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.184 α = 90 b = 102.574 β = 107.19 c = 56.362 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 100 CCD RAYONIX MX-300 2025-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 25 98.5 0.066 16.52 3.6 21662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 0.339
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 2.35 23.81 20582 1059 96.2 0.17634 0.17301 0.24226 0.241 RANDOM 50.613
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] 5.44 2.35 -4.43 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 19.076 r_dihedral_angle_3_deg 15.956 r_long_range_B_other 9.282 r_long_range_B_refined 9.281 r_dihedral_angle_1_deg 7.291 r_scangle_other 7.244 r_mcangle_other 6.195 r_mcangle_it 6.194 r_scbond_other 4.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 19.076 r_dihedral_angle_3_deg 15.956 r_long_range_B_other 9.282 r_long_range_B_refined 9.281 r_dihedral_angle_1_deg 7.291 r_scangle_other 7.244 r_mcangle_other 6.195 r_mcangle_it 6.194 r_scbond_other 4.923 r_scbond_it 4.921 r_mcbond_it 4.286 r_mcbond_other 4.28 r_angle_refined_deg 1.91 r_angle_other_deg 1.294 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 3997 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 237
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SAINT data scaling PHASER phasing