3LBZ
Crystal Structure of the BCL6 BTB domain complexed with the small molecule inhibitor 79-6
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1R29 | PDB ENTRY 1R29 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.3 | 296 | 1 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 | |
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Matthews coefficient | Solvent content |
2.41 | 49.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.712 | α = 90 |
b = 38.611 | β = 114.7 |
c = 78.817 | 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 | ADSC QUANTUM 315 | Rosenbaum-Rock double-crystal monochromator. Rosenbaum-Rock vertical focusing mirror. | 2006-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.979 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 2.3 | 46.225 | 97.5 | 0.066 | 0.052 | 17.86 | 4.1 | 12478 | 12353 | 1 | 49.41 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.3 | 2.4 | 96.9 | 0.158 | 0.14 | 11.36 | 4.1 | 1684 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1R29 | 2.3 | 46.225 | 12477 | 605 | 98.69 | 0.2154 | 0.2154 | 0.2128 | 0.2686 | RANDOM | 42.93 |
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 | -1.16 | 4.13 | -2.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.703 |
r_dihedral_angle_4_deg | 18.221 |
r_dihedral_angle_3_deg | 17.398 |
r_scangle_it | 6.628 |
r_dihedral_angle_1_deg | 6.295 |
r_scbond_it | 3.85 |
r_angle_refined_deg | 2.929 |
r_mcangle_it | 2.709 |
r_mcbond_it | 1.691 |
r_symmetry_hbond_refined | 0.861 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1970 |
Nucleic Acid Atoms | |
Solvent Atoms | 22 |
Heterogen Atoms | 106 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |