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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 4DSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M TrisCl pH 8.0, 0.2 M NaOAc and 30-36 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.12 41.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.085 α = 90 b = 78.085 β = 90 c = 77.65 γ = 120
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 4M 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.45 39.04 100 8.2 5 31312
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 4DSN 1.48 39 27950 1497 99.97 0.17669 0.17522 0.1845 0.20418 0.2125 RANDOM 25.236
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] -0.12 -0.06 -0.12 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.852 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 15.098 r_long_range_B_refined 6.959 r_long_range_B_other 6.945 r_dihedral_angle_1_deg 6.832 r_scangle_other 5.466 r_mcangle_it 3.841 r_mcangle_other 3.839 r_scbond_it 3.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.852 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 15.098 r_long_range_B_refined 6.959 r_long_range_B_other 6.945 r_dihedral_angle_1_deg 6.832 r_scangle_other 5.466 r_mcangle_it 3.841 r_mcangle_other 3.839 r_scbond_it 3.742 r_scbond_other 3.741 r_mcbond_other 2.776 r_mcbond_it 2.775 r_angle_refined_deg 2.254 r_angle_other_deg 1.121 r_chiral_restr 0.14 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 1367 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling EDNA data collection PHASER phasing