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G13D mutant of KRAS4b (2-169) bound to GDP with the switch-I in fully open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M9W 6M9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.4M sodium malonate pH 7
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.076 α = 90 b = 78.076 β = 90 c = 56.197 γ = 120
Symmetry Space Group P 3 2 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 PIXEL DECTRIS EIGER X 16M 2022-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.4 43.22 100 0.071 0.073 0.017 0.999 20.7 19.7 39296
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 1.632 1.675 0.373 0.755 19.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6M9W 1.4 43.26 37309 1984 99.98 0.11857 0.1172 0.1166 0.14426 0.1429 RANDOM 25.131
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] 0.61 0.3 0.61 -1.97
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 15.71 r_dihedral_angle_3_deg 15.079 r_scangle_other 6.087 r_dihedral_angle_2_deg 5.919 r_long_range_B_refined 5.838 r_dihedral_angle_1_deg 5.805 r_scbond_other 5.741 r_scbond_it 5.734 r_long_range_B_other 5.519 r_mcangle_other 3.893
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 15.71 r_dihedral_angle_3_deg 15.079 r_scangle_other 6.087 r_dihedral_angle_2_deg 5.919 r_long_range_B_refined 5.838 r_dihedral_angle_1_deg 5.805 r_scbond_other 5.741 r_scbond_it 5.734 r_long_range_B_other 5.519 r_mcangle_other 3.893 r_mcangle_it 3.869 r_mcbond_other 3.561 r_mcbond_it 3.511 r_angle_refined_deg 1.627 r_angle_other_deg 0.598 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1358 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing