5K29
Trypanosoma brucei bromodomain BDF5 (Tb427tmp.01.5000)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| 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 | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.91 | 35.76 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 53.358 | α = 90 |
| b = 41.02 | β = 111.39 |
| c = 53.067 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |
|---|---|
| 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 | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1311 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 15 |
| Heterogen Atoms | 7 |
Software
| Software | |
|---|---|
| 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 |
