7WN5

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13142


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties
Matthews coefficientSolvent content
1.8332.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.979α = 90
b = 63.61β = 90
c = 72.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray197PIXELDECTRIS PILATUS3 6M2021-01-04MSINGLE 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
11.747.7199.90.1190.1250.040.9988.29.526476
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)
11.71.7399.70.7330.7740.2460.969.5

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 REPLACEMENTTHROUGHOUT4QEW1.747.7124900127898.960.23170.22990.2687RANDOM18.215
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]
0.781.15-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.041
r_dihedral_angle_4_deg21.914
r_dihedral_angle_3_deg11.942
r_dihedral_angle_1_deg5.079
r_angle_refined_deg1.728
r_angle_other_deg0.97
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.041
r_dihedral_angle_4_deg21.914
r_dihedral_angle_3_deg11.942
r_dihedral_angle_1_deg5.079
r_angle_refined_deg1.728
r_angle_other_deg0.97
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1931
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms95

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing