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Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D6E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 SM5-E1+30%Gly
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.927 α = 90 b = 127.927 β = 90 c = 184.655 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 298 PIXEL DECTRIS EIGER X 16M 2022-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.88 100 100 0.168 10 13 24659
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 1.213
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 (All) 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 2.383 95.001 12839 652 54.688 0.207 0.2028 0.2056 0.2898 0.29 RANDOM 62.015
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] 0.028 0.014 0.028 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_3_deg 18.147 r_dihedral_angle_4_deg 17.817 r_lrange_it 9.214 r_lrange_other 9.214 r_dihedral_angle_1_deg 7.208 r_mcangle_other 6.105 r_mcangle_it 6.103 r_scangle_other 6.067 r_scangle_it 6.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_3_deg 18.147 r_dihedral_angle_4_deg 17.817 r_lrange_it 9.214 r_lrange_other 9.214 r_dihedral_angle_1_deg 7.208 r_mcangle_other 6.105 r_mcangle_it 6.103 r_scangle_other 6.067 r_scangle_it 6.064 r_mcbond_it 3.771 r_mcbond_other 3.754 r_scbond_it 3.688 r_scbond_other 3.681 r_angle_refined_deg 1.345 r_angle_other_deg 1.132 r_symmetry_xyhbond_nbd_refined 0.267 r_nbd_refined 0.225 r_nbd_other 0.224 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4341 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing