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Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 2-({3-ethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl}amino)-3-(1H-indol-3-yl)propan-1-ol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 287 Protein concentration 12 mg/mL
Protein Stoarage buffer: 10mM HEPES pH 7.5, 500mM NaCl, 5% Glycerol, 10 mM DTT
Reservoir solution: 5M sodium formate, 6% glycerol
(Protein/reservoir= 1000nL/1000nL)
co-crystallization: added 5 mM chemical and incubated overnight at 4 celsius.
Crystal Properties Matthews coefficient Solvent content 2.05 39.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.573 α = 90 b = 32.454 β = 89.97 c = 79.634 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 CCD ADSC QUANTUM 270 2022-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 50 99.5 0.052 0.073 0.033 0.994 24.878 4.9 51025 12.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 99.9 0.723 0.971 0.442 0.708 1.9 4.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6KEK 1.4 30.54 1.34 45702 1940 94.39 0.178 0.1772 0.1784 0.1963 0.1972 15.41
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 5.2876 f_angle_d 0.9005 f_chiral_restr 0.0736 f_bond_d 0.0063 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2058 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement PHASER phasing HKL-2000 data scaling HKL-2000 data reduction PDB_EXTRACT data extraction