5KO4
Bromodomain from Trypanosoma brucei Tb427.10.8150
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | The 12 mg/ml (0.95 mM) protein in the base buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM HEPES pH7,5) was crystallized at 20 ??C in 30% PEGM5K, 0.2 M NH4SO4, 0.1 M MES pH 6.5, in vapor diffusion sitting drop method. Final concentration of 3% DMSO and 1 mM SGC-CBP30 (IUPAC name: 8-(3-chloro-4-methoxy-phenethyl)-4-(3,5-dimethyl-isoxazol-4-yl)-9-(2-(morpholin-4-yl)-propyl)-7,9-diaza-bicyclo[4.3.0]nona-1(6),2,4,7-tetraene) was added to the concentrated protein immediately prior to setting up the crystallization plate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.374 | α = 90 |
b = 52.756 | β = 117.27 |
c = 47.027 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 300 mm CCD | 2016-04-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97901 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.44 | 50 | 99.2 | 0.082 | 9.1 | 6.7 | 35635 | 15.47 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.44 | 1.46 | 96.5 | 0.358 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3O33 | 1.44 | 41.8 | 35549 | 1865 | 99.2 | 0.162 | 0.161 | 0.176 | RANDOM | 17.65 |
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] | |
0.2775 | -1.3632 | -1.5866 | 1.3092 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 14.85 |
t_omega_torsion | 3.62 |
t_angle_deg | 0.74 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1691 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
HKL-3000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
BALBES | phasing |