5DLZ

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5292Ratio 1:1 (protein:precipitant) 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl.Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M NaNO3. 5.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10% (w/v) glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.1542.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.263α = 90
b = 44.236β = 90
c = 78.436γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2006-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75096.30.1497.544.4714342
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.895.20.4214.154.38

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 REPLACEMENTTHROUGHOUT2OSS1.739.221362471896.290.255290.251220.3339RANDOM12.795
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]
2.46-1.01-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.371
r_dihedral_angle_4_deg24.098
r_sphericity_free19.76
r_dihedral_angle_3_deg14.115
r_sphericity_bonded8.873
r_dihedral_angle_1_deg7.868
r_long_range_B_refined3.128
r_long_range_B_other3.096
r_scangle_other3.087
r_scbond_it2.576
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.371
r_dihedral_angle_4_deg24.098
r_sphericity_free19.76
r_dihedral_angle_3_deg14.115
r_sphericity_bonded8.873
r_dihedral_angle_1_deg7.868
r_long_range_B_refined3.128
r_long_range_B_other3.096
r_scangle_other3.087
r_scbond_it2.576
r_scbond_other2.574
r_rigid_bond_restr2.423
r_angle_refined_deg2.329
r_mcangle_it2.251
r_mcangle_other2.251
r_mcbond_it1.957
r_mcbond_other1.949
r_angle_other_deg1.473
r_chiral_restr0.135
r_bond_refined_d0.028
r_gen_planes_refined0.012
r_bond_other_d0.007
r_gen_planes_other0.002
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 Atoms1062
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms34

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement