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Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF 3mxf, 5fqd experimental model PDB 5FQD 3mxf, 5fqd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Crystal Properties Matthews coefficient Solvent content 3.71 66.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.571 α = 90 b = 115.571 β = 90 c = 596.315 γ = 120
Symmetry Space Group P 65 2 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 PILATUS 6M-F 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
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 3.49 49.87 99.5 0.128 0.14 0.055 0.999 11.4 11.4 31460
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 3.49 3.68 97.3 3.561 3.924 1.173 0.328 0.7 10.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3mxf, 5fqd 3.501 49.868 1.33 30441 1454 97.87 0.2143 0.2123 0.2179 0.2555 0.2571 Random selection
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 14.956 f_angle_d 0.481 f_chiral_restr 0.042 f_bond_d 0.007 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10268 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing