3S92

Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor JQ1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OO1PDB entry 2OO1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720% PEG 3350, 0.2M (NH4)2Hcit, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0439.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.36α = 90
b = 38.02β = 90
c = 85.79γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
11.3628.45299.90.0680.06811.44.4242052418113
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)
11.361.4399.90.730.731.14.53446

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 2OO11.3628.452420024149123399.790.13420.13420.13140.1865RANDOM16.1558
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]
0.28-0.05-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.565
r_dihedral_angle_4_deg24.897
r_sphericity_free14.772
r_dihedral_angle_3_deg12.453
r_scangle_it8.545
r_scbond_it6.998
r_sphericity_bonded6.524
r_dihedral_angle_1_deg5.529
r_mcangle_it4.99
r_mcbond_it3.884
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.565
r_dihedral_angle_4_deg24.897
r_sphericity_free14.772
r_dihedral_angle_3_deg12.453
r_scangle_it8.545
r_scbond_it6.998
r_sphericity_bonded6.524
r_dihedral_angle_1_deg5.529
r_mcangle_it4.99
r_mcbond_it3.884
r_rigid_bond_restr3.359
r_mcbond_other2.344
r_angle_refined_deg1.642
r_angle_other_deg0.974
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms903
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms35

Software

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