3MXF

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JQ1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.2M NaI 0.1M BTProp pH 8.5 20% PEG3350 10% EtGhly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.8α = 90
b = 44.76β = 90
c = 78.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.542

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
11.626.82899.70.0460.04618.64.1177161766314.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6998.50.1370.166.93.62467

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 2OSS1.626.83176871760989499.560.1510.1510.150.184RANDOM14.011
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]
0.42-0.12-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.993
r_dihedral_angle_3_deg12.506
r_dihedral_angle_4_deg12.292
r_scangle_it5.323
r_dihedral_angle_1_deg5.006
r_scbond_it3.96
r_mcangle_it2.802
r_mcbond_it1.795
r_angle_refined_deg1.698
r_angle_other_deg0.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.993
r_dihedral_angle_3_deg12.506
r_dihedral_angle_4_deg12.292
r_scangle_it5.323
r_dihedral_angle_1_deg5.006
r_scbond_it3.96
r_mcangle_it2.802
r_mcbond_it1.795
r_angle_refined_deg1.698
r_angle_other_deg0.965
r_mcbond_other0.551
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1059
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms48

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction