3UVY

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52780.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
1.7128.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.225α = 90
b = 50.478β = 90
c = 51.969γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9793DiamondI03

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
12.0243.22599.70.1350.1358.64.27890786622.9
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)
12.022.131000.8310.8310.94.41118

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 REPLACEMENTTHROUGHOUTEnsemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C2.0243.227857782845999.630.18560.18560.18110.2582RANDOM28.0894
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]
2.16-1.92-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.371
r_dihedral_angle_3_deg14.719
r_scangle_it11.273
r_scbond_it9.15
r_dihedral_angle_4_deg6.687
r_mcangle_it5.857
r_dihedral_angle_1_deg5.585
r_mcbond_it4.034
r_angle_refined_deg1.525
r_mcbond_other1.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.371
r_dihedral_angle_3_deg14.719
r_scangle_it11.273
r_scbond_it9.15
r_dihedral_angle_4_deg6.687
r_mcangle_it5.857
r_dihedral_angle_1_deg5.585
r_mcbond_it4.034
r_angle_refined_deg1.525
r_mcbond_other1.264
r_angle_other_deg1.009
r_chiral_restr0.081
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms

Software

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