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Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CD8 experimental model PDB 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
Crystal Properties Matthews coefficient Solvent content 2.97 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.855 α = 103.09 b = 87.613 β = 90.9 c = 88.44 γ = 106.23
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2023-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978530 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 47.81 97.07 0.09 9.97 3.5 34488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.01 0.528
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 2.9 38.46 1.98 34141 1713 97.13 0.2388 0.2355 0.2438 0.301 0.3014
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 13.331 f_angle_d 1.759 f_chiral_restr 0.078 f_plane_restr 0.017 f_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8030 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 317
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing