2OUO

Crystal Structure of the Bromo domain 2 in human Bromodomain Containing Protein 4 (BRD4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X0JPDB entry 1X0J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.1M MIB, 30% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.032α = 90
b = 73.698β = 90
c = 33.467γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2007-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54000

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
11.7473.7299.30.0650.06511.43.71512515125
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)
11.741.7898.60.6183.31156

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1X0J1.8950120301203072298.160.1840.1840.1820.216RANDOM27.303
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]
-0.260.180.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.577
r_dihedral_angle_4_deg26.097
r_dihedral_angle_3_deg11.279
r_dihedral_angle_1_deg5.308
r_scangle_it2.936
r_scbond_it2.144
r_angle_refined_deg1.531
r_mcangle_it1.455
r_mcbond_it1.053
r_angle_other_deg1.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.577
r_dihedral_angle_4_deg26.097
r_dihedral_angle_3_deg11.279
r_dihedral_angle_1_deg5.308
r_scangle_it2.936
r_scbond_it2.144
r_angle_refined_deg1.531
r_mcangle_it1.455
r_mcbond_it1.053
r_angle_other_deg1.048
r_mcbond_other0.316
r_symmetry_vdw_other0.292
r_nbd_refined0.22
r_symmetry_vdw_refined0.215
r_nbd_other0.183
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.139
r_chiral_restr0.09
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms882
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction