5HM0

Crystal structure of the first bromodomain of human BRD4 bound to benzoisoxazoloazepine 3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2773.4-3.8 M sodium formate, 0.1 M Tris pH 7.8, and 10% glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.0840.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.682α = 90
b = 47.722β = 90
c = 78.184γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.3955099.20.06522.66.525403
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)
11.3951.4694.60.5835.1

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 REPLACEMENTTHROUGHOUT2OSS1.39540.7324051129298.180.192050.190240.22619RANDOM32.161
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]
5.34-3.39-1.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.235
r_dihedral_angle_3_deg14.704
r_dihedral_angle_4_deg8.652
r_long_range_B_refined7.031
r_long_range_B_other7.028
r_dihedral_angle_1_deg6.427
r_scangle_other5.68
r_scbond_it3.932
r_scbond_other3.929
r_mcangle_other2.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.235
r_dihedral_angle_3_deg14.704
r_dihedral_angle_4_deg8.652
r_long_range_B_refined7.031
r_long_range_B_other7.028
r_dihedral_angle_1_deg6.427
r_scangle_other5.68
r_scbond_it3.932
r_scbond_other3.929
r_mcangle_other2.932
r_mcangle_it2.915
r_mcbond_it2.258
r_mcbond_other2.152
r_angle_refined_deg1.486
r_angle_other_deg0.784
r_chiral_restr0.099
r_gen_planes_refined0.016
r_bond_refined_d0.012
r_gen_planes_other0.001
r_bond_other_d
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 Atoms1042
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing