6YQZ
N-terminal domain of BRD4 with biphenyl-methyamino-dimethylpyridazinone
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 20%w/v PEG 3350, 0.2M sodium sulphate,0.1M bis-tris-propane (pH 6.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.94 | α = 90 |
b = 44.37 | β = 90 |
c = 78.05 | 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 | PIXEL | DECTRIS PILATUS 2M | 2012-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.97625 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.39 | 39.03 | 98.5 | 0.083 | 0.094 | 0.043 | 9 | 4.1 | 26727 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.39 | 1.47 | 95.2 | 0.513 | 0.513 | 0.619 | 0.338 | 1.5 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | In house structure | 1.39 | 39.03 | 25379 | 1348 | 98.17 | 0.1732 | 0.1717 | 0.2037 | RANDOM | 18.245 |
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] | |
1.52 | -0.44 | -1.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.96 |
r_dihedral_angle_3_deg | 12.568 |
r_dihedral_angle_4_deg | 10.168 |
r_dihedral_angle_1_deg | 5.547 |
r_angle_other_deg | 1.27 |
r_angle_refined_deg | 1.194 |
r_chiral_restr | 0.062 |
r_gen_planes_refined | 0.005 |
r_bond_refined_d | 0.004 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1062 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |