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Structure of IKZF2:CRBN:Compound 5 ternary structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.2 M Magnesium chloride
0.1 M TRIS pH 8.5
33 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.16 α = 90 b = 70.18 β = 90.01 c = 78.71 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS EIGER2 X 16M 2022-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
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 1.86 46.2 98.7 0.3 0.325 0.123 0.992 8.9 6.8 41050
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 1.87 1.91 94.1 0.91 1.002 0.412 0.839 5.6
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 FOURIER SYNTHESIS THROUGHOUT 1.86 46.2 39620 2032 98.41 0.17734 0.17525 0.1867 0.21758 0.2268 RANDOM 19.661
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] -0.38 -0.4 2.84 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.077 r_dihedral_angle_2_deg 10.272 r_dihedral_angle_1_deg 6.574 r_long_range_B_refined 5.863 r_long_range_B_other 5.835 r_scangle_other 4.148 r_mcangle_other 2.938 r_mcangle_it 2.936 r_scbond_it 2.601 r_scbond_other 2.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.077 r_dihedral_angle_2_deg 10.272 r_dihedral_angle_1_deg 6.574 r_long_range_B_refined 5.863 r_long_range_B_other 5.835 r_scangle_other 4.148 r_mcangle_other 2.938 r_mcangle_it 2.936 r_scbond_it 2.601 r_scbond_other 2.601 r_mcbond_it 1.858 r_mcbond_other 1.856 r_angle_refined_deg 1.531 r_angle_other_deg 0.521 r_chiral_restr 0.075 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4258 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing