3UVW
Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac)
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 PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2OUO | Ensemble of PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2GRC | Ensemble of PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2OO1 | Ensemble of PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 3DAI | Ensemble of PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 3D7C | Ensemble of PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 278 | 0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.87 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 42.5 | ¦Á = 90 |
b = 47.28 | ¦Â = 90 |
c = 59.53 | ¦Ã = 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 | CCD | ADSC QUANTUM 315r | 2010-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9763 | Diamond | I04 |
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 | 1.37 | 37.01 | 99.6 | 0.1 | 0.1 | 10 | 5.5 | 25922 | 25818 | 11.7 |
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 | 1.37 | 1.44 | 97.2 | 0.52 | 0.52 | 1.5 | 3.1 | 3617 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C | 1.37 | 37.01 | 25894 | 25770 | 1312 | 99.52 | 0.1269 | 0.1269 | 0.1246 | 0.1711 | RANDOM | 14.0345 |
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] | |
0.02 | 0.27 | -0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.121 |
r_dihedral_angle_4_deg | 14.141 |
r_sphericity_free | 13.067 |
r_dihedral_angle_3_deg | 12.196 |
r_scangle_it | 8.004 |
r_scbond_it | 5.897 |
r_dihedral_angle_1_deg | 5.85 |
r_sphericity_bonded | 5.188 |
r_mcangle_it | 4.5 |
r_mcbond_it | 3.489 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1137 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
GDA | data collection |
MOSFLM | data reduction |