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Crystal Structure of human KRAS G12V in complex with GDP and AM-2383
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 200mM ammonium sulfate, 100mM sodium acetate, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.25 45.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.265 α = 90 b = 53.657 β = 90 c = 87.917 γ = 90
Symmetry Space Group P 21 21 21
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 2022-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 98.4 0.08 0.99 11.13 3.7 113385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.27 94.6 0.157 0.957 5.14 3
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 1.2 30 56754 2961 98.9 0.19342 0.19243 0.2014 0.21218 0.2189 RANDOM 11.679
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] 0.18 -0.24 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.215 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_3_deg 11.036 r_dihedral_angle_1_deg 6.206 r_long_range_B_refined 4.115 r_long_range_B_other 3.526 r_angle_refined_deg 1.416 r_angle_other_deg 1.31 r_scangle_other 1.238 r_mcangle_it 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.215 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_3_deg 11.036 r_dihedral_angle_1_deg 6.206 r_long_range_B_refined 4.115 r_long_range_B_other 3.526 r_angle_refined_deg 1.416 r_angle_other_deg 1.31 r_scangle_other 1.238 r_mcangle_it 0.964 r_mcangle_other 0.964 r_scbond_it 0.785 r_scbond_other 0.785 r_mcbond_it 0.552 r_mcbond_other 0.552 r_chiral_restr 0.055 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_bond_other_d 0.001 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 1353 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 85
Software Software Software Name Purpose XDS data reduction XDS data scaling REFMAC refinement Coot model building MOLREP phasing