7WNI

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13158


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 Sodium malonate pH 4.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
3.7767.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.685α = 90
b = 108.685β = 90
c = 81.58γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray197PIXELDECTRIS PILATUS3 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
13.1276.8599.90.3010.3320.1360.79845.59140
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)
13.123.341000.7390.8130.3310.8195.5

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 REPLACEMENTTHROUGHOUT6E6J3.1276.85865446199.750.21040.20780.2575RANDOM46.485
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]
-5.34-5.3410.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.515
r_dihedral_angle_4_deg23.79
r_dihedral_angle_3_deg19.181
r_dihedral_angle_1_deg6.227
r_angle_refined_deg1.711
r_angle_other_deg0.989
r_chiral_restr0.073
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.515
r_dihedral_angle_4_deg23.79
r_dihedral_angle_3_deg19.181
r_dihedral_angle_1_deg6.227
r_angle_refined_deg1.711
r_angle_other_deg0.989
r_chiral_restr0.073
r_bond_refined_d0.016
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 Atoms1802
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms107

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing