3UVY
Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OSS | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2OUO | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2GRC | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2OO1 | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 3DAI | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 3D7C | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 278 | 0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.71 | 28.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.225 | α = 90 |
b = 50.478 | β = 90 |
c = 51.969 | 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 | ADSC QUANTUM 315r | 2011-01-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9793 | Diamond | I03 |
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 | 2.02 | 43.225 | 99.7 | 0.135 | 0.135 | 8.6 | 4.2 | 7890 | 7866 | 22.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.02 | 2.13 | 100 | 0.831 | 0.831 | 0.9 | 4.4 | 1118 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C | 2.02 | 43.22 | 7857 | 7828 | 459 | 99.63 | 0.1856 | 0.1856 | 0.1811 | 0.2582 | RANDOM | 28.0894 |
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] | |
2.16 | -1.92 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.371 |
r_dihedral_angle_3_deg | 14.719 |
r_scangle_it | 11.273 |
r_scbond_it | 9.15 |
r_dihedral_angle_4_deg | 6.687 |
r_mcangle_it | 5.857 |
r_dihedral_angle_1_deg | 5.585 |
r_mcbond_it | 4.034 |
r_angle_refined_deg | 1.525 |
r_mcbond_other | 1.264 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 65 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
GDA | data collection |
XDS | data reduction |