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Crystal structure of KRAS G12D D38C (GDP-bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium nitrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.978 α = 90 b = 66.978 β = 90 c = 89.466 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS EIGER X 16M 2023-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.54184 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 53.618 95.8 1 19.2 16.1 23560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.71 0.4
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 1.64 53.618 22425 1135 92.74 0.14614 0.14409 0.1587 0.1852 0.1941 RANDOM 20.596
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.394 r_long_range_B_other 13.155 r_dihedral_angle_3_deg 10.732 r_scangle_other 9.053 r_mcangle_other 7.415 r_mcangle_it 7.401 r_scbond_other 6.338 r_scbond_it 6.329 r_dihedral_angle_1_deg 5.459 r_mcbond_it 5.118
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.394 r_long_range_B_other 13.155 r_dihedral_angle_3_deg 10.732 r_scangle_other 9.053 r_mcangle_other 7.415 r_mcangle_it 7.401 r_scbond_other 6.338 r_scbond_it 6.329 r_dihedral_angle_1_deg 5.459 r_mcbond_it 5.118 r_mcbond_other 5.066 r_dihedral_angle_2_deg 3.821 r_rigid_bond_restr 3.407 r_angle_refined_deg 1.543 r_angle_other_deg 0.558 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 1395 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing