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Crystal Structure of small molecule beta-lactone 1 covalently bound to K-Ras(G12S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6USZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1 M sodium acetate, 30% w/v PEG MME 2K, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.78 α = 90 b = 50.66 β = 90 c = 89.31 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2021-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.999881 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.98716752773 89.31 99 0.999 21.4 11.9 12881 28.2008098411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98716752773 2.04 95.8 0.896
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 FREE R-VALUE 6USZ 1.98716752773 44.6549 1.34110029439 12843 636 98.8835848476 0.191293951803 0.189088453173 0.1919 0.233787340602 0.2372 29.5360900052
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_dihedral_angle_d 18.5983855174 f_angle_d 1.0524158486 f_chiral_restr 0.0540754829276 f_bond_d 0.00693075880117 f_plane_restr 0.00444869085231
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1421 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection iMOSFLM data reduction Aimless data scaling PHENIX phasing PHENIX refinement