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Crystal structure of KRAS-G12D/K104Q 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 7.3 293 3.0 % Xylitol, 0.2 M ammonium acetate and 2.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.93 α = 90 b = 84.93 β = 90 c = 89.3 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 PILATUS 6M-F 2019-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 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 1.84 44.65 100 0.119 0.129 0.994 10.09 6.89 62031 35.229
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 1.84 1.95 100 0.555 0.602 0.779 2.69 7.04
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5US4 1.84 44.65 59030 2995 99.04 0.1345 0.1333 0.158 0.1824 RANDOM 30.044
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] -7.66 -7.66 15.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.349 r_dihedral_angle_4_deg 17.247 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 5.939 r_angle_refined_deg 1.561 r_angle_other_deg 1.283 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.349 r_dihedral_angle_4_deg 17.247 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 5.939 r_angle_refined_deg 1.561 r_angle_other_deg 1.283 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5340 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 132
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing