4E96

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor PFi-1


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 Na(malonate) 0.1M BTProp pH 8.5 20% PEG3350 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.141.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.71α = 90
b = 46.71β = 90
c = 78.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

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
11.9123.35599.50.110.118.84.6104641041226.5
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)
11.912.01990.8190.8190.94.61479

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 2OSS1.9223.35102081012548999.190.21590.21590.21260.2855RANDOM28.7881
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]
4-2.1-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.106
r_dihedral_angle_3_deg15.524
r_dihedral_angle_4_deg15.075
r_scangle_it9.941
r_scbond_it8.435
r_dihedral_angle_1_deg5.849
r_mcangle_it5.556
r_mcbond_it4.251
r_angle_refined_deg1.512
r_mcbond_other1.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.106
r_dihedral_angle_3_deg15.524
r_dihedral_angle_4_deg15.075
r_scangle_it9.941
r_scbond_it8.435
r_dihedral_angle_1_deg5.849
r_mcangle_it5.556
r_mcbond_it4.251
r_angle_refined_deg1.512
r_mcbond_other1.421
r_angle_other_deg0.991
r_chiral_restr0.079
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1020
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms33

Software

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