5NNF

Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated BAZ1B peptide (K221ac)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527720% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 8.5 0.02M sodium/potassium phosphate
Crystal Properties
Matthews coefficientSolvent content
238.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.439α = 90
b = 43.915β = 90
c = 79.69γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.1529.5199.10.0370.0370.0150.01533.96.847482
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)
11.151.2199.30.0840.08415.55.86775

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 REPLACEMENTTHROUGHOUT2OSS1.1529.5145469194699.850.120020.118930.14448RANDOM12.17
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]
0.78-0.33-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.026
r_sphericity_free19.017
r_dihedral_angle_4_deg13.75
r_dihedral_angle_3_deg12.823
r_sphericity_bonded6.513
r_dihedral_angle_1_deg5.846
r_long_range_B_refined2.501
r_long_range_B_other2.187
r_scangle_other2.117
r_rigid_bond_restr1.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.026
r_sphericity_free19.017
r_dihedral_angle_4_deg13.75
r_dihedral_angle_3_deg12.823
r_sphericity_bonded6.513
r_dihedral_angle_1_deg5.846
r_long_range_B_refined2.501
r_long_range_B_other2.187
r_scangle_other2.117
r_rigid_bond_restr1.924
r_scbond_other1.722
r_scbond_it1.721
r_angle_refined_deg1.715
r_mcangle_other1.479
r_mcangle_it1.476
r_mcbond_it1.155
r_mcbond_other1.144
r_angle_other_deg1.088
r_chiral_restr0.112
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1119
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building