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KRAS-G12D(1-169) - GDP IN covalent COMPLEX WITH compound (3R,4R)-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30 % PEG 1000, 0.2 M MgSO4
Crystal Properties Matthews coefficient Solvent content 2.45 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.367 α = 90 b = 51.924 β = 90 c = 90.419 γ = 90
Symmetry Space Group P 21 21 21
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 2023-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00002 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.55 45.21 94.3 0.172 5.9 9.8 21979
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.69 60.4 1.448 1.5 9.2
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 1NFQI 1.546 45.21 21979 1091 77 0.1864 0.185 0.1814 0.2133 0.2167 RANDOM 24.36
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] 0.9947 -0.4791 -0.5156
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.76 t_omega_torsion 3.68 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1310 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 88
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing