5CRZ

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 DROP827720% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
1.9436.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.92α = 90
b = 47.34β = 90
c = 78.37γ = 90
Symmetry
Space GroupP 21 21 21

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
12.1278.3794.10.0970.0390.99310.87.47346
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)
12.122.1899.70.2510.0940.9855.78.1640

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 REPLACEMENTTHROUGHOUT3MXF2.1240.52693537593.60.22740.22580.2567RANDOM32.145
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]
6.55-2.82-3.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.983
r_dihedral_angle_3_deg12.855
r_dihedral_angle_4_deg10.809
r_dihedral_angle_1_deg5.243
r_mcangle_it1.306
r_angle_refined_deg1.108
r_angle_other_deg0.883
r_mcbond_other0.726
r_mcbond_it0.725
r_chiral_restr0.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.983
r_dihedral_angle_3_deg12.855
r_dihedral_angle_4_deg10.809
r_dihedral_angle_1_deg5.243
r_mcangle_it1.306
r_angle_refined_deg1.108
r_angle_other_deg0.883
r_mcbond_other0.726
r_mcbond_it0.725
r_chiral_restr0.054
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1115
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing