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KRAS G12D (GppCp) with MRTX-1133
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RPZ PDB entry 7RPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Bis-Tris, pH 5.5, 0.1 M sodium acetate, 8% v/v isopropanol, 22% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.311 α = 90 b = 50.579 β = 90 c = 92.903 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 2021-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.27 46.4515 94.48 0.04256 0.01824 0.999 26.3 6.5 48107 11.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.315 88.63 0.1862 0.07941 0.984
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 7RPZ 1.27 46.45 1.4 48103 2355 94.35 0.1533 0.1523 0.1545 0.1724 0.1734 16.81
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 14.4871 f_angle_d 1.6205 f_chiral_restr 0.1006 f_plane_restr 0.0174 f_bond_d 0.0157
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1349 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 115
Software Software Software Name Purpose PHENIX refinement PHENIX refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing