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Human HRAS 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 293 0.2M Magnesium acetate, 20.0% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.935 α = 90 b = 48.772 β = 109.53 c = 65.546 γ = 90
Symmetry Space Group C 1 2 1
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 1.076 64.057 93.5 0.0695 0.0785 0.0359 0.997 10.2 4.61 117556
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) 1.076 1.199 68.5 0.8828 1.0148 0.4916 0.639 1.6 4.06 5878
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 1.08 64.057 1.35 117546 5937 67.19 0.1891 0.1882 0.1875 0.2061 0.2055 14.8778
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 2866 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 110
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