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Human KRAS G12D (GDP-bound) in complex with macrocyclic peptide inhibitor AP2527
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 4.6 293 0.1M Sodium acetate trihydrate (pH 4.6), 8.0 %w/v Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.476 α = 90 b = 66.476 β = 90 c = 86.805 γ = 120
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 2025-01-22 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 1.7 57.57 94.4 0.197 0.2028 0.0477 0.999 9.09 17.75 17465
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) 1.701 1.91 53.9 3.2324 3.3401 0.8371 0.557 1.48 15.54 873
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 THROUGHOUT 7YV1 1.7 57.57 1.35 17463 890 73.09 0.1972 0.195 0.1949 0.2393 0.2391 30.9644
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 1457 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 63
Software Software Software Name Purpose autoPROC data processing XDS data reduction STARANISO data scaling Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction