4YH4
Crystal structure of human BRD4(1) in complex with 4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19d)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | 0.2 M potassium thiocyanate, 20% w/v PEG3350, 0.6 mM ligand |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.799 | α = 90 |
b = 44.436 | β = 90 |
c = 77.353 | 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 | 2012-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9300 | NSLS | X29A |
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 | 1.33 | 50 | 99.9 | 0.067 | 17.8 | 13.8 | 30557 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.33 | 1.38 | 100 | 0.308 | 11.3 | 14 | 2983 |
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 | 1.33 | 33.96 | 30417 | 1538 | 99.58 | 0.1093 | 0.1073 | 0.1466 | RANDOM | 17.0817 |
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] | |
0.1 | 0.04 | -0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.889 |
r_sphericity_free | 33.12 |
r_dihedral_angle_3_deg | 12.79 |
r_sphericity_bonded | 12.053 |
r_dihedral_angle_4_deg | 11.144 |
r_dihedral_angle_1_deg | 6.234 |
r_rigid_bond_restr | 5.953 |
r_angle_refined_deg | 2.316 |
r_mcangle_it | 2.156 |
r_mcbond_it | 1.772 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1061 |
Nucleic Acid Atoms | |
Solvent Atoms | 249 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |