3LBZ

Crystal Structure of the BCL6 BTB domain complexed with the small molecule inhibitor 79-6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.32961 microliter of protein solution (9.5 mg/ml BCL6-BTB in 20 mM Tris pH 8.3, 450 mM NaCl, 1 mM TCEP) was mixed with 1 microliter of reservoir solution (180 mM sodium acetate, 190 mM sodium formate, 10% Glycerol, 50 mM NaCl and 10mM N-(4-bromophenylsulfonyl)acetamide), VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.4149.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.712α = 90
b = 38.611β = 114.7
c = 78.817γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Rosenbaum-Rock double-crystal monochromator. Rosenbaum-Rock vertical focusing mirror.2006-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
12.346.22597.50.0660.05217.864.11247812353149.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.496.90.1580.1411.364.11684

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1R292.346.2251247760598.690.21540.21540.21280.2686RANDOM42.93
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]
-2.49-1.164.13-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.703
r_dihedral_angle_4_deg18.221
r_dihedral_angle_3_deg17.398
r_scangle_it6.628
r_dihedral_angle_1_deg6.295
r_scbond_it3.85
r_angle_refined_deg2.929
r_mcangle_it2.709
r_mcbond_it1.691
r_symmetry_hbond_refined0.861
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.703
r_dihedral_angle_4_deg18.221
r_dihedral_angle_3_deg17.398
r_scangle_it6.628
r_dihedral_angle_1_deg6.295
r_scbond_it3.85
r_angle_refined_deg2.929
r_mcangle_it2.709
r_mcbond_it1.691
r_symmetry_hbond_refined0.861
r_symmetry_vdw_refined0.333
r_nbtor_refined0.318
r_nbd_refined0.249
r_chiral_restr0.148
r_xyhbond_nbd_refined0.11
r_bond_refined_d0.03
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1970
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms106

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling