5BT4

Crystal structure of BRD4 first bromodomain in complex with SGC-CBP30 chemical probe


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1 M succinic acid, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4249.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.923α = 90
b = 91.801β = 90
c = 113.761γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.571.4499.60.0980.03414.49.769534671462
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5292.80.4264.88.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.571.4467816356799.620.192350.19120.21425RANDOM17.298
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]
-0.170.29-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.043
r_dihedral_angle_4_deg14.249
r_dihedral_angle_3_deg11.888
r_dihedral_angle_1_deg4.738
r_long_range_B_other4.271
r_long_range_B_refined4.27
r_scangle_other2.11
r_angle_refined_deg1.422
r_scbond_it1.324
r_scbond_other1.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.043
r_dihedral_angle_4_deg14.249
r_dihedral_angle_3_deg11.888
r_dihedral_angle_1_deg4.738
r_long_range_B_other4.271
r_long_range_B_refined4.27
r_scangle_other2.11
r_angle_refined_deg1.422
r_scbond_it1.324
r_scbond_other1.323
r_mcangle_it1.249
r_mcangle_other1.248
r_angle_other_deg0.939
r_mcbond_it0.773
r_mcbond_other0.772
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3152
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing