6G0P

Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated E2F1 peptide (K117ac/K120ac)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727720.0 % PEG3350 10.0 % EtGly 0.2 M NaCHO
Crystal Properties
Matthews coefficientSolvent content
2.1642.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.137α = 90
b = 53.358β = 90
c = 58.126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.358.12699.90.0340.0360.01429.66.73448834488
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)
11.31.3799.60.1760.1760.1970.0874.54.9

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, 3DWY1.339.3132631179699.910.12610.12490.1473RANDOM16.906
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]
0.110.79-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.524
r_dihedral_angle_4_deg24.806
r_sphericity_free20.381
r_dihedral_angle_3_deg11.558
r_sphericity_bonded6.638
r_dihedral_angle_1_deg5.502
r_rigid_bond_restr2.332
r_angle_refined_deg1.616
r_angle_other_deg0.995
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.524
r_dihedral_angle_4_deg24.806
r_sphericity_free20.381
r_dihedral_angle_3_deg11.558
r_sphericity_bonded6.638
r_dihedral_angle_1_deg5.502
r_rigid_bond_restr2.332
r_angle_refined_deg1.616
r_angle_other_deg0.995
r_chiral_restr0.114
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1110
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms4

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction