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Crystal structure of KRAS-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 293 0.1 M Tris pH 8.5 and 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.56 α = 90 b = 84.56 β = 90 c = 88.36 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 1.59 44.18 99.7 0.076 0.085 0.997 11.33 5.097 94111 32.816
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 1.59 1.69 99.8 0.717 0.803 0.755 2.01 5.116
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 5US4 1.59 44.18 89343 4764 99.69 0.1823 0.1816 0.1813 0.1954 0.1943 RANDOM 25.685
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] -7.63 -7.63 15.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.731 r_dihedral_angle_4_deg 13.806 r_dihedral_angle_3_deg 12.35 r_dihedral_angle_1_deg 5.928 r_angle_refined_deg 1.372 r_angle_other_deg 1.267 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.731 r_dihedral_angle_4_deg 13.806 r_dihedral_angle_3_deg 12.35 r_dihedral_angle_1_deg 5.928 r_angle_refined_deg 1.372 r_angle_other_deg 1.267 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5315 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 152
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing