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Structure of CRBN TBD bound to compound C3
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 291 0.2M tri-Sodium citrate
18 % w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 3.36 63.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.559 α = 90 b = 86.279 β = 114.42 c = 90.972 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 2022-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 2.61 60.36 62.6 0.99 7 4.1 12509
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 2.61 2.85 0.293
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 2.61 60.36 11895 614 62.52 0.21642 0.21484 0.2174 0.24802 0.2472 RANDOM 65.14
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] 1.22 0.28 -0.91 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.696 r_dihedral_angle_2_deg 11.962 r_dihedral_angle_1_deg 7.24 r_long_range_B_refined 5.067 r_long_range_B_other 5.066 r_mcangle_it 3.015 r_mcangle_other 3.015 r_scangle_other 2.511 r_mcbond_it 1.658 r_mcbond_other 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.696 r_dihedral_angle_2_deg 11.962 r_dihedral_angle_1_deg 7.24 r_long_range_B_refined 5.067 r_long_range_B_other 5.066 r_mcangle_it 3.015 r_mcangle_other 3.015 r_scangle_other 2.511 r_mcbond_it 1.658 r_mcbond_other 1.658 r_scbond_it 1.351 r_scbond_other 1.351 r_angle_refined_deg 1.02 r_angle_other_deg 0.336 r_chiral_restr 0.047 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3393 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PDB_EXTRACT data extraction FFT phasing