5EIS
FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-(4-Chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OSS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 292 | ratio 1:1 (protein:precipitant). 16 mg/mL Brd4_BD1 protein. 2.5 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.1M HEPES (pH 7.5) 0.15 mM NaCl. Precipitant agent: 19% (w/v) PEG 3350, 0.25M ammonium sulfate, 0.1M Tris pH 8.5. Cryoprotectant: 10% (w/v) ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.935 | α = 90 |
b = 46.545 | β = 90 |
c = 77.658 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS PILATUS 2M | 2007-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.87260 | ESRF | ID23-2 |
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 | 1.6 | 50 | 99.4 | 0.054 | 14.87 | 4.6 | 17766 |
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 | 1.6 | 1.7 | 98.7 | 0.558 | 2.73 | 4.7 |
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 | 2OSS | 1.6 | 39.92 | 16876 | 889 | 99.41 | 0.18448 | 0.18269 | 0.2191 | RANDOM | 27.433 |
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] | |
4.27 | -1.48 | -2.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.202 |
r_dihedral_angle_4_deg | 20.966 |
r_dihedral_angle_3_deg | 14.352 |
r_long_range_B_other | 6.379 |
r_long_range_B_refined | 6.377 |
r_dihedral_angle_1_deg | 6.276 |
r_scangle_other | 4.768 |
r_mcangle_other | 3.553 |
r_mcangle_it | 3.537 |
r_scbond_it | 3.413 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1062 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
REFMAC | refinement |