5DX4

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 DROP727720% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4549.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.83α = 90
b = 48.44β = 90
c = 77.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97852SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.377.4296.30.1140.9899.24.56577
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3895.30.1880.9695.14.3617

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 REPLACEMENTTHROUGHOUT3MXF2.341.06623731395.20.21660.21540.2391RANDOM25.229
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]
4.49-1.19-3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.284
r_dihedral_angle_3_deg15.096
r_dihedral_angle_4_deg10.48
r_dihedral_angle_1_deg5.493
r_mcangle_it1.8
r_angle_refined_deg1.302
r_mcbond_it1.102
r_mcbond_other1.101
r_angle_other_deg0.931
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.284
r_dihedral_angle_3_deg15.096
r_dihedral_angle_4_deg10.48
r_dihedral_angle_1_deg5.493
r_mcangle_it1.8
r_angle_refined_deg1.302
r_mcbond_it1.102
r_mcbond_other1.101
r_angle_other_deg0.931
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1048
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing