5CY9

Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MXF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.827720% PEG3350, 0.2M NaCl, 0.1M HEPES, 10% EtGhly,pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.5752.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.05α = 90
b = 54.05β = 90
c = 50.69γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONOTHER0.97852

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.5546.8190.50.0640.0230.99914.77.821754
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5895.20.3560.1550.9343.25.91109

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 REPLACEMENTTHROUGHOUT3MXF1.5546.8120541119290.520.165010.163170.19788RANDOM19.902
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]
-0.33-0.17-0.331.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.061
r_dihedral_angle_4_deg17.072
r_dihedral_angle_3_deg11.307
r_long_range_B_refined5.075
r_long_range_B_other5.073
r_dihedral_angle_1_deg5.012
r_scangle_other3.355
r_scbond_it2.072
r_scbond_other2.072
r_mcangle_it1.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.061
r_dihedral_angle_4_deg17.072
r_dihedral_angle_3_deg11.307
r_long_range_B_refined5.075
r_long_range_B_other5.073
r_dihedral_angle_1_deg5.012
r_scangle_other3.355
r_scbond_it2.072
r_scbond_other2.072
r_mcangle_it1.939
r_mcangle_other1.937
r_angle_refined_deg1.512
r_mcbond_it1.213
r_mcbond_other1.213
r_angle_other_deg1.087
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1091
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing