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First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 46
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Protein solution:10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 46
Crystallization condition: 25% PEG 3350, 0.3 M sodium malonate pH 7, 10% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.913 α = 90 b = 48.912 β = 109.12 c = 73.043 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2023-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.71 69.01 99.5 0.074 0.03 0.999 13.2 7 51876 23.5818360234
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 0.941 0.385 0.71 1.9
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 1.71000018061 42.0231746928 1.33788976398 51845 2631 99.3808464959 0.196060877397 0.194105205283 0.1938 0.232074470539 0.2314 27.552207263
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 11.6726270764 f_angle_d 0.875875343791 f_chiral_restr 0.0453501593658 f_plane_restr 0.00780992413609 f_bond_d 0.00690597329787
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 224
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing