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Human KRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2M Magnesium chloride, 0.1M Tris (pH 8.5), 25.0% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.43 α = 87.21 b = 45.025 β = 89.83 c = 57.779 γ = 65.79
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 2024-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.99999 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.445 57.7 83.5 0.0723 0.1015 0.0712 0.988 3.4 1.89 31129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.445 1.774 33 0.5092 0.7154 0.5019 0.6 1.68 1.94 1556
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 THROUGHOUT 1.45 57.7 1.98 31119 1499 45.71 0.1944 0.1929 0.1895 0.2248 0.2232 17.1049
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2927 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 80
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction