7WMU

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13146


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QEW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
1.9737.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.41α = 90
b = 35.57β = 96.51
c = 73.563γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray197PIXELDECTRIS PILATUS 6M2021-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

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
11.7342.4599.10.1140.1260.0520.99213.55.613041
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)
11.731.7698.10.8190.9050.3770.7725.6

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 REPLACEMENTTHROUGHOUT4QEW1.7342.451237565698.70.15180.15010.1847RANDOM16.534
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]
0.78-0.29-0.35-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.51
r_dihedral_angle_4_deg23.67
r_dihedral_angle_3_deg13.127
r_dihedral_angle_1_deg4.694
r_angle_refined_deg1.782
r_angle_other_deg1.252
r_chiral_restr0.092
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.51
r_dihedral_angle_4_deg23.67
r_dihedral_angle_3_deg13.127
r_dihedral_angle_1_deg4.694
r_angle_refined_deg1.782
r_angle_other_deg1.252
r_chiral_restr0.092
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms921
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms86

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing