5D0C

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 DROP7.527720% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9536.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.03α = 90
b = 46.27β = 96.74
c = 47.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97915SSRFBL17U

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
11.4947.1190.80.060.0260.99623.9719102
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)
11.491.5296.50.10.0410.99315.26.9986

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 REPLACEMENTTHROUGHOUT3MXF1.4947.111821387490.690.16540.16450.1833RANDOM15.264
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]
-0.32-0.260.47-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.395
r_dihedral_angle_3_deg12.899
r_dihedral_angle_4_deg9.624
r_dihedral_angle_1_deg5.043
r_mcangle_it1.683
r_angle_refined_deg1.583
r_angle_other_deg1.054
r_mcbond_it1.029
r_mcbond_other1.028
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.395
r_dihedral_angle_3_deg12.899
r_dihedral_angle_4_deg9.624
r_dihedral_angle_1_deg5.043
r_mcangle_it1.683
r_angle_refined_deg1.583
r_angle_other_deg1.054
r_mcbond_it1.029
r_mcbond_other1.028
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1072
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms55

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing