5EK9

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP527720% PEG6000, 0.1M citrate pH5
Crystal Properties
Matthews coefficientSolvent content
2.7555.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.704α = 90
b = 69.749β = 90
c = 141.215γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9794DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.0829.2199.40.1590.06713.112.61791017910
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.1492.80.83.111.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0829.211696391499.390.183940.181830.190.223120.23RANDOM30.351
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]
0.64-0.32-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.458
r_dihedral_angle_4_deg19.816
r_dihedral_angle_3_deg15.171
r_long_range_B_other5.727
r_long_range_B_refined5.725
r_dihedral_angle_1_deg5.222
r_scangle_other4.21
r_mcangle_other2.623
r_mcangle_it2.62
r_scbond_it2.574
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1776
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing