7RV5

Crystal structure of the BCL6 BTB domain in complex with OICR-9287


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R29 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5292Precipitant solution was 16-20% PEG 8K in 0.1M pH 6.5 Hepes buffer, 50 mM CaCl2 with microseeding. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to passage through paratone and freezing. Crystals grew as large doubly birefringent rods which were gently crushed. Singly birefringent pieces were selected for data collection.
Crystal Properties
Matthews coefficientSolvent content
2.0138.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.62α = 90
b = 72.198β = 105.97
c = 55.079γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.2152.9599.60.0940.1310.0993.3576928.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.370.4830.6650.4562.1

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1R292.2136.1576957699.330.16880.16260.225933.37
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.1202
f_angle_d1.2347
f_chiral_restr0.0843
f_bond_d0.0134
f_plane_restr0.0086
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms981
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms34

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing