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Structure of CRBN TBD bound to compound C1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 277 0.2M tri-Sodium citrate
18 % w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 3.29 62.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.35 α = 90 b = 87.61 β = 113.98 c = 89.5 γ = 90
Symmetry Space Group C 1 2 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 16M 2023-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.42 46.84 89.9 0.999 16.2 6.9 20893
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.5 0.681
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 MOLECULAR REPLACEMENT THROUGHOUT 2.42 43.84 20893 1098 89.9 0.18506 0.18261 0.1884 0.22761 0.2346 RANDOM 56.179
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] -0.17 0.13 0.1 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.805 r_long_range_B_other 11.646 r_long_range_B_refined 11.645 r_scangle_other 9.022 r_dihedral_angle_1_deg 7.911 r_mcangle_it 7.425 r_mcangle_other 7.423 r_dihedral_angle_2_deg 7.141 r_scbond_it 6.155 r_scbond_other 6.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.805 r_long_range_B_other 11.646 r_long_range_B_refined 11.645 r_scangle_other 9.022 r_dihedral_angle_1_deg 7.911 r_mcangle_it 7.425 r_mcangle_other 7.423 r_dihedral_angle_2_deg 7.141 r_scbond_it 6.155 r_scbond_other 6.153 r_mcbond_it 5.154 r_mcbond_other 5.154 r_angle_refined_deg 1.718 r_angle_other_deg 0.595 r_chiral_restr 0.088 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3383 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PDB_EXTRACT data extraction FFT phasing