Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13157
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6VIW | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277 | 1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane pH 7.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.8 | 67.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 141.205 | α = 90 |
| b = 141.205 | β = 90 |
| c = 132.727 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 197 | PIXEL | DECTRIS PILATUS3 6M | 2021-10-05 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.97911 | SSRF | BL02U1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.73 | 44.97 | 99.4 | 0.083 | 0.092 | 0.039 | 0.997 | 12.9 | 5.4 | 21133 | |||||||||
| 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 | 2.73 | 2.86 | 100 | 0.747 | 0.833 | 0.363 | 0.829 | 5.2 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6viw | 2.73 | 44.97 | 20064 | 1045 | 99.11 | 0.1826 | 0.1809 | 0.19 | 0.2149 | 0.22 | RANDOM | 79.584 | ||||
| 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] | |
| -2.84 | -1.42 | -2.84 | 9.21 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.555 |
| r_dihedral_angle_3_deg | 16.891 |
| r_dihedral_angle_4_deg | 12.825 |
| r_dihedral_angle_1_deg | 5.518 |
| r_angle_refined_deg | 1.462 |
| r_angle_other_deg | 1.093 |
| r_chiral_restr | 0.075 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_refined | 0.006 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2724 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 18 |
| Heterogen Atoms | 174 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Aimless | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MOLREP | phasing |
