7WLN

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13153


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6E6J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2778% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
3.7567.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.97α = 90
b = 95.762β = 90
c = 110.085γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray197PIXELDECTRIS PILATUS3 6M2021-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97852SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.8572.2599.60.20.2440.0910.9826.46.922992
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.85399.90.8910.9580.3470.7457.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6E6J2.8572.2521777116899.390.18590.18350.2315RANDOM49.128
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]
3.98-2.14-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.619
r_dihedral_angle_3_deg18.28
r_dihedral_angle_4_deg17.567
r_dihedral_angle_1_deg5.155
r_angle_refined_deg1.643
r_angle_other_deg1.07
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.619
r_dihedral_angle_3_deg18.28
r_dihedral_angle_4_deg17.567
r_dihedral_angle_1_deg5.155
r_angle_refined_deg1.643
r_angle_other_deg1.07
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3607
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms213

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing