2OSS

Crystal structure of the Bromo domain 1 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 DROP7.52770.2M NaNO3, 20% PEG3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.418α = 90
b = 44.139β = 90
c = 78.413γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97910SLSX10SA

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
11.355099.90.0710.07114.18.12934929320
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)
11.351.41000.1776.52874

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 1X0J1.3539.192928029262148599.940.150.150.1490.174RANDOM8.628
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]
0.16-0.02-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.633
r_dihedral_angle_3_deg10.633
r_dihedral_angle_4_deg8.232
r_dihedral_angle_1_deg5.497
r_sphericity_free3.78
r_scangle_it2.903
r_scbond_it2.091
r_sphericity_bonded2.046
r_mcangle_it1.528
r_angle_refined_deg1.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.633
r_dihedral_angle_3_deg10.633
r_dihedral_angle_4_deg8.232
r_dihedral_angle_1_deg5.497
r_sphericity_free3.78
r_scangle_it2.903
r_scbond_it2.091
r_sphericity_bonded2.046
r_mcangle_it1.528
r_angle_refined_deg1.298
r_rigid_bond_restr1.144
r_mcbond_it1.112
r_angle_other_deg0.909
r_mcbond_other0.354
r_symmetry_vdw_refined0.291
r_symmetry_vdw_other0.278
r_nbd_refined0.219
r_nbtor_refined0.189
r_nbd_other0.171
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.094
r_nbtor_other0.09
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1047
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms12

Software

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