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Crystal structure of GDP-bound human K-RAS in a covalent complex with aryl sulfonyl fluoride compounds.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium chloride 0.2 M and PEG 3350 20%
Crystal Properties Matthews coefficient Solvent content 2.04 39.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.867 α = 90 b = 83.885 β = 90 c = 104.689 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 CMOS RDI CMOS_8M 2021-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0722 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.67 104.69 96.3 0.089 0.105 0.055 0.998 9 3.7 69748 11.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 96.9 0.885 1.036 0.535 0.596 1.1
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 FREE R-VALUE 1.67 52.34 20.99 65190 3326 90.04 0.2743 0.2703 0.2617 0.2886 0.2685 20.41
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]
RMS Deviations Key Refinement Restraint Deviation f_angle_d 0.6928 f_chiral_restr 0.0446 f_plane_restr 0.0045 f_bond_d 0.0033 f_dihedral_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5310 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 192
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing