8WY3

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 21


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7WJS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52772.0 M Sodium formate, 0.1 M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.867.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.409α = 90
b = 140.409β = 90
c = 134.482γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 6M2023-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL10U20.97918SSRFBL10U2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.78134.48970.2240.2320.0580.996915.619675
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.782.931001.2891.3370.3490.85814.4

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 REPLACEMENTTHROUGHOUT7wjs2.78121.61869293996.950.187970.185760.2336RANDOM63.77
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]
-3.15-1.58-3.1510.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.802
r_dihedral_angle_3_deg20.137
r_dihedral_angle_4_deg13.148
r_long_range_B_refined11.307
r_long_range_B_other11.307
r_scangle_other8.681
r_mcangle_other7.879
r_mcangle_it7.878
r_dihedral_angle_1_deg6.115
r_scbond_it5.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.802
r_dihedral_angle_3_deg20.137
r_dihedral_angle_4_deg13.148
r_long_range_B_refined11.307
r_long_range_B_other11.307
r_scangle_other8.681
r_mcangle_other7.879
r_mcangle_it7.878
r_dihedral_angle_1_deg6.115
r_scbond_it5.427
r_scbond_other5.426
r_mcbond_it5.127
r_mcbond_other5.126
r_angle_refined_deg1.978
r_angle_other_deg1.19
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms2806
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing