7WNA

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13120


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.6152.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.63α = 90
b = 106.63β = 90
c = 87.97γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray197PIXELDECTRIS PILATUS3 6M2020-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97892SSRFBL19U1

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
12.6106.6398.80.1260.1410.0610.9927.9530036
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)
12.62.721000.670.7470.3250.6925.3

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 REPLACEMENTTHROUGHOUT6E6J2.6106.6328466156298.670.21160.20850.2683RANDOM56.596
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]
1.541.54-3.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_4_deg18.14
r_dihedral_angle_3_deg18.097
r_dihedral_angle_1_deg6.085
r_angle_refined_deg1.694
r_angle_other_deg1.029
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_4_deg18.14
r_dihedral_angle_3_deg18.097
r_dihedral_angle_1_deg6.085
r_angle_refined_deg1.694
r_angle_other_deg1.029
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5369
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms292

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing