6FSY

Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSSEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OUOEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental modelPDB 2GRCEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OO1Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DAIEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental modelPDB 3D7CEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DWYEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527720 % PEG 3350 and 0.1 M citrate pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1743.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.316α = 90
b = 42.91β = 90
c = 79.797γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96861DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.33829.2299.70.0780.0780.0850.03411.36.230364
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.4198.10.5630.5630.6230.2631.35.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY1.3429.2228822143099.840.15750.15550.1997RANDOM19.083
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]
0.65-0.38-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.278
r_dihedral_angle_4_deg26.213
r_sphericity_free20.174
r_dihedral_angle_3_deg12.497
r_sphericity_bonded9.186
r_dihedral_angle_1_deg5.941
r_rigid_bond_restr2.411
r_angle_refined_deg1.715
r_angle_other_deg1.042
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.278
r_dihedral_angle_4_deg26.213
r_sphericity_free20.174
r_dihedral_angle_3_deg12.497
r_sphericity_bonded9.186
r_dihedral_angle_1_deg5.941
r_rigid_bond_restr2.411
r_angle_refined_deg1.715
r_angle_other_deg1.042
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1049
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms30

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction