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Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 8-15% w/v Polyethylene Glycol 3350 and 0.2 M lithium citrate
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.6 α = 90 b = 118.76 β = 90 c = 156.9 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 PILATUS3 6M 2016-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.66 59.38 100 0.108 0.032 0.999 13.6 13.4 140853
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3GFT 1.66 59.38 133751 7000 99.99 0.17989 0.17855 0.1892 0.20544 0.2148 RANDOM 35.755
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] -0.78 1.09 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.997 r_dihedral_angle_4_deg 18.585 r_dihedral_angle_3_deg 13.786 r_long_range_B_other 10.185 r_long_range_B_refined 10.183 r_scangle_other 8.312 r_dihedral_angle_1_deg 5.602 r_scbond_it 5.573 r_scbond_other 5.572 r_mcangle_it 5.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.997 r_dihedral_angle_4_deg 18.585 r_dihedral_angle_3_deg 13.786 r_long_range_B_other 10.185 r_long_range_B_refined 10.183 r_scangle_other 8.312 r_dihedral_angle_1_deg 5.602 r_scbond_it 5.573 r_scbond_other 5.572 r_mcangle_it 5.439 r_mcangle_other 5.439 r_mcbond_it 3.962 r_mcbond_other 3.958 r_angle_refined_deg 2.137 r_angle_other_deg 1.095 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8221 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 339
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling Coot model building