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Crystal structure of KRAS-G75A 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 2.2 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.93 α = 90 b = 84.93 β = 90 c = 87.65 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 EIGER X 16M 2022-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 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 2 50 99.9 0.13 0.14400000000000002 0.99 7.95 5.3 47789
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 2 2.05 1.13 1.2570000000000001 0.5670000000000001
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 2 43.83 45448 2340 99.91 0.1641 0.16264 0.1561 0.19231 0.1844 RANDOM 38.77
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] -15.88 -15.88 31.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.833 r_dihedral_angle_3_deg 14.585 r_long_range_B_refined 6.441 r_dihedral_angle_1_deg 5.718 r_mcangle_it 3.167 r_scbond_it 2.18 r_mcbond_it 2.124 r_angle_refined_deg 1.147 r_chiral_restr 0.088 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.833 r_dihedral_angle_3_deg 14.585 r_long_range_B_refined 6.441 r_dihedral_angle_1_deg 5.718 r_mcangle_it 3.167 r_scbond_it 2.18 r_mcbond_it 2.124 r_angle_refined_deg 1.147 r_chiral_restr 0.088 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5322 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing