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The crystal structure of KRAS G12D (GDP bound) in complex with RP03519
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 20%~30% PEG 8000, 200 mM ammonium acetate, 100 mM Tri-sodium citrate pH 4.2,
Crystal Properties Matthews coefficient Solvent content 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.214 α = 90 b = 53.372 β = 90 c = 88.598 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 9M 2023-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 1.316 30.195 91.1 0.999 20.3 6.9 41893
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 1.316 1.339 64.8 0.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.32 30.19 1.34 41891 2049 91.1 0.1842 0.1833 0.1844 0.2019 0.2008
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.621 f_angle_d 0.958 f_chiral_restr 0.076 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1348 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHENIX phasing