7LZQ
Crystal structure of the BCL6 BTB domain in complex with OICR-4425
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Protein (Bcl6 BTB domain(1-129) 13 mg/ml in protein buffer( 20 mM Tris pH 8.3, 300 mM NaCl, 10% glycerol, 1 mM TECEP)) was mixed 1:1 with reservoir buffer (1.3M sodium formate, 0.1M Na acetate pH 5.2. Ostwald ripening of the early appearing crystals took place over about 5 days. To affect a partial dehydration the reservoir buffer was exchanged in 0.5 M steps to 4 M Na formate/0.1M Na acetate pH 5.2. In separate wells drops of soaking buffer ((1 M Na formate, 5% glycerol, 50 mM Na acetate pH5.2, 10 mM Tris pH 8.3, 150 mM NaCl) was also equilibrated against the 4 M formate/acetate. Crystals were transferred to equilibrated soaking buffer to which 2.5 mM OICR-4425 and 5% DMSO had been added. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 37.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.412 | α = 90 |
b = 71.626 | β = 104.782 |
c = 54.937 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | APEX II CCD | 2011-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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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) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 1.71 | 27.21 | 96.8 | 0.026 | 0.03 | 0.015 | 0.999 | 30.7 | 3.9 | 12163 | 16.44 |
Highest Resolution Shell | |||||||||||||||||||
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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) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.71 | 1.74 | 80.5 | 0.127 | 0.153 | 0.083 | 0.989 | 7.6 | 3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1R28 | 1.71 | 27.2 | 1.36 | 11936 | 564 | 96.77 | 0.1578 | 0.156 | 0.1936 | 23.69 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.9246 |
f_angle_d | 1.674 |
f_chiral_restr | 0.0953 |
f_bond_d | 0.0146 |
f_plane_restr | 0.0095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1024 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |