7RUI
Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with XR844
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 1.6 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 0.1 M sodium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.158 | α = 90 |
b = 42.303 | β = 90 |
c = 90.557 | 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 EIGER X 9M | 2021-04-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.0332 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.35 | 42.3 | 97 | 0.081 | 0.089 | 0.036 | 0.995 | 11.7 | 5.9 | 31930 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.35 | 1.37 | 77.5 | 0.363 | 0.438 | 0.239 | 0.832 | 3.2 |
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 | PDB entry 3MXF | 1.35 | 38.36 | 30290 | 1586 | 96.6 | 0.1702 | 0.1692 | 0.1895 | RANDOM | 17.917 |
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] | |
1.53 | -0.74 | -0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.848 |
r_dihedral_angle_4_deg | 16.01 |
r_dihedral_angle_3_deg | 14.13 |
r_dihedral_angle_1_deg | 5.837 |
r_angle_refined_deg | 1.954 |
r_angle_other_deg | 1.478 |
r_chiral_restr | 0.097 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.013 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1065 |
Nucleic Acid Atoms | |
Solvent Atoms | 119 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |