3UVX
Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K12acK16ac)
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 | 7.5 | 278 | 0.35M NaFortmate 20% PEG 3350 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.23 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 43.94 | ¦Á = 90 |
b = 52.38 | ¦Â = 90 |
c = 57.62 | ¦Ã = 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2010-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.52 |
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 | 1.91 | 24.09 | 99.9 | 0.112 | 0.112 | 8.1 | 4.4 | 10815 | 10804 | 26.6 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.91 | 2.01 | 100 | 0.617 | 0.617 | 1.2 | 4.2 | 1538 |
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 | 1.91 | 24.09 | 10780 | 10766 | 517 | 99.87 | 0.1697 | 0.1697 | 0.1672 | 0.2187 | RANDOM | 27.8702 |
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] | |
-0.82 | 1.06 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.096 |
r_dihedral_angle_4_deg | 18.329 |
r_dihedral_angle_3_deg | 14.969 |
r_dihedral_angle_1_deg | 5.959 |
r_angle_refined_deg | 1.471 |
r_angle_other_deg | 0.951 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.007 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1101 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
MOSFLM | data reduction |