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Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GDP and Covalently Bound to an Adduct of (2S)-1-{4-[(7P)-7-(8-ethynyl-7-fluoro-3-hydroxynaphthalen-1-yl)-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]piperazin-1-yl}-2-fluoro-3-(1,3-thiazol-2-yl)propan-1-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 100 MM Sodium acetate anhydrous, pH 4.6, 200 MM ammonium sulfate, 25% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.095 α = 90 b = 50.928 β = 90 c = 90.182 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 PIXEL DECTRIS EIGER X 9M 2023-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92000 NSLS-II 17-ID-1
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 1.504 45.091 91.8 0.0819 0.0855 0.0241 0.999 14.92 11.33 25968
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) 1.504 1.591 43.9 0.9885 1.0999 0.4664 0.521 1.34 5.31 1299
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.504 17.48 25943 1295 86.3 0.2064 0.2055 0.1999 0.2242 0.219 RANDOM 26.22
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] 0.1892 -0.1658 -0.0234
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.66 t_omega_torsion 3.46 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1351 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 80
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling BUSTER refinement AMoRE phasing