5K29
Trypanosoma brucei bromodomain BDF5 (Tb427tmp.01.5000)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 12% PEG-3350, 0.1M DL-Malic acid. 0.001 M Bromosporine was also added but not located in the electron density. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.91 | 35.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.358 | α = 90 |
b = 41.02 | β = 111.39 |
c = 53.067 | 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 | 2015-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0000 | APS | 22-ID |
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 | 2.1 | 49.68 | 99.5 | 0.047 | 0.055 | 0.029 | 0.998 | 14.3 | 3.7 | 12642 | 50.19 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 2.16 | 99.9 | 1.092 | 1.276 | 0.654 | 0.745 | 1.4 | 3.8 | 1061 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.1 | 49.41 | 12631 | 1225 | 99.4 | 0.194 | 0.191 | 0.223 | 72.06 |
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] | |
-3.7765 | 15.7011 | 5.05 | -1.2735 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.64 |
t_omega_torsion | 2.48 |
t_angle_deg | 0.96 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1311 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
BUSTER-TNT | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
XDS | data scaling |
BUCCANEER | model building |
PHASER | phasing |
SHELXDE | phasing |
ARP | model building |
WARP | model building |