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Structure of CRBN:IKZF2:Compound 15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.04 α = 90 b = 70.13 β = 90 c = 78.74 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 100 PIXEL DECTRIS EIGER X 9M 2022-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9001 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 20.1 97.47 0.147 0.998 11.6 12.7 61174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.987 0.814 8.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 20.1 61174 3273 97.47 0.17351 0.17195 0.20148 0.205 RANDOM 17.234
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.129 r_dihedral_angle_2_deg 10.175 r_dihedral_angle_1_deg 6.636 r_long_range_B_refined 5.853 r_long_range_B_other 5.755 r_scangle_other 4.482 r_scbond_it 2.864 r_scbond_other 2.863 r_mcangle_it 2.855 r_mcangle_other 2.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.129 r_dihedral_angle_2_deg 10.175 r_dihedral_angle_1_deg 6.636 r_long_range_B_refined 5.853 r_long_range_B_other 5.755 r_scangle_other 4.482 r_scbond_it 2.864 r_scbond_other 2.863 r_mcangle_it 2.855 r_mcangle_other 2.855 r_mcbond_it 1.946 r_mcbond_other 1.915 r_angle_refined_deg 1.682 r_angle_other_deg 0.588 r_chiral_restr 0.086 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4286 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing