6AFR

Crystal Structure of the first bromodomain of human BRD4 in complex with 5-((4-fluoro-1H-imidazol-1-yl)methyl)quinolin-8-ol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4289.15The protein was concentrated to 8-10 mg mL-1 in the buffer containing 20mM HEPES, pH7.4, 100mM NaCl and 1mM DTT. The apo crystals of BRD4_BD1 were harvested by using sitting drop vapor-diffusion method in 4M sodium formate and 15% glycerol at 289.15K. Then the apo crystals were soaked into reservoir solution containing 1mM compound for 7 days.
Crystal Properties
Matthews coefficientSolvent content
1.9737.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.98α = 90
b = 47.208β = 90
c = 78.737γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDNonius Kappa CCD2018-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.99839.3799.8212.4412.68538
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9982.069

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.99839.371.34853341699.840.21450.21160.2677
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.92
f_angle_d0.911
f_chiral_restr0.049
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1047
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms18

Software

Software
Software NamePurpose
PHENIXrefinement