8BPT
Crystal structure of the second bromodomain of BRD5 from Leishmania donovani
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 0.1 M HEPES pH 7.5 and 1.4 M sodium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.37 | α = 90 |
b = 75.356 | β = 90 |
c = 105.798 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2018-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.6 | 31.845 | 98.3 | 0.047 | 0.054 | 0.025 | 0.999 | 19.4 | 8.1 | 35399 |
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 | 1.6 | 1.63 | 0.568 | 0.646 | 0.304 | 0.928 | 8.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5TCK | 1.6 | 31.845 | 35358 | 1701 | 97.893 | 0.164 | 0.1615 | 0.2147 | 17.081 |
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] | |
2.076 | -2.183 | 0.107 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.436 |
r_dihedral_angle_3_deg | 15.855 |
r_dihedral_angle_2_deg | 11.057 |
r_dihedral_angle_1_deg | 4.694 |
r_scangle_it | 4.371 |
r_scangle_other | 4.37 |
r_rigid_bond_restr | 4.154 |
r_lrange_it | 4.153 |
r_lrange_other | 4.13 |
r_scbond_it | 3.951 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2212 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data scaling |
xia2 | data reduction |
pointless | data scaling |
Coot | model building |