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Human KRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AUBE00
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 6.5 293 0.2M Sodium sulfate, 0.1M BIS-Tris propane (pH 6.5), 20.0 %(w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.61 65.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.031 α = 90 b = 144.031 β = 90 c = 181.173 γ = 90
Symmetry Space Group I 4 2 2
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 2024-10-16 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 1.558 112.744 95.2 0.2464 0.2571 0.073 0.997 9.6 12.3 103683
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) 1.558 1.715 61.9 5.0191 5.2272 1.4502 0.526 1.41 12.72 5184
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 1.56 67.69 1.34 103666 5175 77.07 0.178 0.1769 0.1771 0.1995 0.1997 24.4455
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 4473 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 229
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction