5N2M

Crystal structure of the first bromodomain of human BRD4 in complex with a tetrahydroquinoline analogue


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M NH4SO4, 25% PEG3350, 0.1M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.550.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.797α = 90
b = 42.09β = 90
c = 92.576γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9794DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.5429.7598.80.20.136.76227447.081
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.5781.10.5120.3494.74.9

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 REPLACEMENTTHROUGHOUT2OSS1.5429.7521570112398.670.198560.196960.23018RANDOM10.766
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]
-0.05-0.030.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.592
r_dihedral_angle_4_deg18.905
r_dihedral_angle_3_deg10.591
r_dihedral_angle_1_deg5.429
r_angle_refined_deg1.563
r_angle_other_deg0.846
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.592
r_dihedral_angle_4_deg18.905
r_dihedral_angle_3_deg10.591
r_dihedral_angle_1_deg5.429
r_angle_refined_deg1.563
r_angle_other_deg0.846
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1062
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing