4XYA
Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-amine-9H-purine ligand
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 8.5, 0.2M sodium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.242 | α = 90 |
b = 44.373 | β = 90 |
c = 79.015 | 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 | CCD | APEX II CCD | 2014-11-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.05 | 44.37 | 99.9 | 0.08 | 0.08 | 12.37 | 4.73 | 8708 |
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 | 2.05 | 2.09 | 99.7 | 0.235 | 3.05 |
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 | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.05 | 39.51 | 8237 | 433 | 99.93 | 0.1496 | 0.1466 | 0.2068 | RANDOM | 14.528 |
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] | |
0.48 | -0.39 | -0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.111 |
r_dihedral_angle_3_deg | 12.633 |
r_dihedral_angle_4_deg | 12.214 |
r_sphericity_bonded | 11.348 |
r_dihedral_angle_1_deg | 5.779 |
r_mcangle_it | 2.701 |
r_mcbond_it | 1.808 |
r_mcbond_other | 1.807 |
r_angle_refined_deg | 1.652 |
r_angle_other_deg | 0.915 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1056 |
Nucleic Acid Atoms | |
Solvent Atoms | 148 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |