☰ Navigation Tabs
Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N-[2-(1H-indol-3-yl)ethyl]-3-(trifluoromethyl)[1,2,4]triazolo[4,3-b]pyridazin-6-amine
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 storage buffer: 10 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol 10 mM DTT
Reservoir solution: 6M sodium formate, 6% glycerol
Protein: reservoir solution=1:1
co-crystallization: added 5mM chemical and incubated overnight at 4 celsius
Crystal Properties Matthews coefficient Solvent content 2.03 39.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.498 α = 90 b = 32.398 β = 89.99 c = 79.474 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 PILATUS 6M 2022-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.979 PAL/PLS 11C
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 1.5 50 97.6 0.061 0.066 0.025 0.999 25.85 6.6 38524 12.28
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 1.5 1.53 89.9 0.289 0.314 0.123 0.962 5.4 5.8
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 1.5 47.5 1.34 37174 1995 93.82 0.1803 0.1791 0.1795 0.2005 0.1989 14.28
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 10.345 f_angle_d 0.9413 f_chiral_restr 0.0745 f_bond_d 0.0068 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2058 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement PHASER phasing HKL-2000 data scaling HKL-2000 data reduction PDB_EXTRACT data extraction