4CP3

The structure of BCL6 BTB (POZ) domain in complex with the ansamycin antibiotic rifabutin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R2BPDB ENTRY 1R2B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1520% PEG 6000, 100MM SODIUM CITRATE, PH 5.
Crystal Properties
Matthews coefficientSolvent content
1.9938.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.172α = 90
b = 54.828β = 95.21
c = 58.159γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.339.82970.1089.8391684.1
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)
12.32.38970.5184.12.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1R2B2.357.92916846697.130.201930.198770.26875RANDOM29.366
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]
1.85-0.01-0.11-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.034
r_dihedral_angle_4_deg19.575
r_dihedral_angle_3_deg17.089
r_dihedral_angle_1_deg6.623
r_mcangle_it3.032
r_scbond_it2.594
r_angle_refined_deg1.875
r_mcbond_it1.848
r_mcbond_other1.84
r_angle_other_deg0.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.034
r_dihedral_angle_4_deg19.575
r_dihedral_angle_3_deg17.089
r_dihedral_angle_1_deg6.623
r_mcangle_it3.032
r_scbond_it2.594
r_angle_refined_deg1.875
r_mcbond_it1.848
r_mcbond_other1.84
r_angle_other_deg0.863
r_chiral_restr0.171
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1969
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing