5EGU
FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-Butyl-8-(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylsulfanylmethyl)-7-ethyl-3,7-dihydropurine-2,6-dione
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2OSS |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 292 | Ratio 1:1 (protein:precipitant). 25 mg/mL BRD4_BD1 protein. 1.0 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350. Cryoprotectant : 10% ethylene glycol. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.59 | 52.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 69.686 | α = 90 |
b = 83.612 | β = 90 |
c = 107.391 | γ = 90 |
Symmetry | |
---|---|
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 | IMAGE PLATE | MAR scanner 345 mm plate | 2006-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.541790 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 50 | 97.8 | 0.104 | 13.15 | 4.63 | 59187 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.21 | 2.35 | 95.2 | 0.48 | 3.44 | 4.52 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2OSS | 2.21 | 45.18 | 29752 | 1566 | 97.87 | 0.18724 | 0.18474 | 0.2353 | RANDOM | 25.187 |
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] | |
0.39 | 0.67 | -1.06 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.462 |
r_dihedral_angle_4_deg | 14.513 |
r_dihedral_angle_3_deg | 14.214 |
r_dihedral_angle_1_deg | 6.442 |
r_long_range_B_refined | 5.644 |
r_long_range_B_other | 5.644 |
r_scangle_other | 4.27 |
r_mcangle_it | 3.246 |
r_mcangle_other | 3.246 |
r_scbond_it | 2.7 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3934 |
Nucleic Acid Atoms | |
Solvent Atoms | 250 |
Heterogen Atoms | 140 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
REFMAC | refinement |