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First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45
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 45
Crystallization condition: 24% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Crystal Properties Matthews coefficient Solvent content 2.05 40.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.396 α = 90 b = 48.683 β = 109.429 c = 73 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 0.9405 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 1.9 68.843 99.3 0.088 0.036 0.999 12 7.1 37837 28.4313423131
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 1.9 1.94 0.931 0.387 0.673 2
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 1.90001265923 68.8429723154 1.33649196202 37788 1907 99.129066107 0.198111700066 0.195980548291 0.1968 0.236766004086 0.2381 30.446492613
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 10.7493615573 f_angle_d 0.923846802781 f_chiral_restr 0.0467487567254 f_plane_restr 0.00789355022074 f_bond_d 0.00784303874179
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4045 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 172
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing