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Crystal structure of CRBN-midi in complex with mezigdomide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 214 uM mezigdomide
0.2 M sodium acetate, 25% (w/v) PEG 3350, and 0.1 M BIS-TRIS pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.046 α = 90 b = 51.046 β = 90 c = 267.677 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2022-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.00 Diamond I24
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 2.19 66.9 91.8 0.989 6.4 6.5 13035 38.24
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 2.19 2.37 0.53
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 2.19 40.59 1.34 13032 649 67.55 0.2589 0.2576 0.2577 0.285 0.2857 41.45
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 18.9832 f_angle_d 1.3282 f_chiral_restr 0.071 f_bond_d 0.0093 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction STARANISO data scaling PHASER phasing Coot model building