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Human NRAS 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 Sodium phosphate monobasic, 20.0% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.873 α = 90 b = 61.594 β = 99.4 c = 83.712 γ = 90
Symmetry Space Group P 1 21 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 1.232 82.588 91.2 0.0567 0.0674 0.0361 0.997 7.71 3.36 123736
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) 1.232 1.385 48.5 1.1883 1.4307 0.7862 0.402 1.52 3.08 6187
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 1.232 49.37 1.34 123714 6226 67.99 0.1972 0.1963 0.1959 0.2129 0.2125 20.8569
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 4331 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 156
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