3U5L

Crystal Structure of the first bromodomain of human BRD4 in complex with a benzo-triazepine ligand (BzT-7)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.20M Na(malonate), 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.36α = 90
b = 44.13β = 90
c = 78.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.38829.396.90.0630.06318.66.726798259678.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.391.4696.90.2390.2393.16.93709

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OSS1.3929.32679825820130796.350.11240.11240.11070.1419RANDOM11.2602
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]
0.4-0.22-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.631
r_sphericity_free21.277
r_dihedral_angle_4_deg14.387
r_dihedral_angle_3_deg11.017
r_sphericity_bonded7.456
r_dihedral_angle_1_deg5.537
r_rigid_bond_restr3.022
r_angle_refined_deg1.7
r_angle_other_deg0.909
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.631
r_sphericity_free21.277
r_dihedral_angle_4_deg14.387
r_dihedral_angle_3_deg11.017
r_sphericity_bonded7.456
r_dihedral_angle_1_deg5.537
r_rigid_bond_restr3.022
r_angle_refined_deg1.7
r_angle_other_deg0.909
r_chiral_restr0.083
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1055
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms27

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction