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Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TZX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.114 α = 90 b = 145.029 β = 90 c = 191.895 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 S 9M 2021-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 3.35 52.48 98.7 0.283 0.289 0.059 0.998 9.8 23.3 44026
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 3.35 3.48 100 4.452 4.586 1.077 0.28 17.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.35 46.88 1.97 43910 2207 98.67 0.2057 0.2022 0.2102 0.2709 0.2701
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.457 f_angle_d 1.048 f_chiral_restr 0.055 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17543 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing