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First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 14
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, 1 mM degrader 14.
Crystallization condition: 25% PEG 3350, 0.25 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.2.
Crystal Properties Matthews coefficient Solvent content 1.95 36.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.881 α = 90 b = 50.473 β = 90 c = 58.494 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2021-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.13 38.88 99.4 0.059 0.999 16.9 9.4 43620 11.5707962251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.15 0.694 0.901 3.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.13003035503 38.2135195985 1.35061396929 43557 2204 99.3816738158 0.159129533173 0.157876033539 0.1697 0.184990601247 0.1874 5 17.2190893888
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 11.4984001162 f_angle_d 0.799521117603 f_chiral_restr 0.0698762420743 f_plane_restr 0.00575786680839 f_bond_d 0.0047537532577
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1028 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing