4FLP
Crystal Structure of the first bromodomain of human BRDT in complex with the inhibitor JQ1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2RFJ | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2OSS | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2OUO | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2GRC | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2OO1 | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 3DAI | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 3D7C | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 3DWY | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | 0.1M BisTris propane pH 8.0, 0.15M KSCN, 25% PEG3350, 10% EtGly , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.44 | 49.59 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 37.4 | ¦Á = 90 |
b = 57.42 | ¦Â = 90 |
c = 128.69 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | P 21 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2011-01-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 37.4 | 99.5 | 0.11 | 0.11 | 7.2 | 3.4 | 14729 | 14655 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 2.32 | 99.9 | 0.655 | 0.655 | 1.1 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Ensemble of 2RFJ, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY | 2.23 | 42.84 | 14168 | 13419 | 708 | 99.71 | 0.21343 | 0.21113 | 0.25487 | RANDOM | 37.929 |
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] | |
0.42 | -0.49 | 0.07 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.596 |
r_dihedral_angle_3_deg | 18.006 |
r_scangle_it | 11.799 |
r_dihedral_angle_4_deg | 11.536 |
r_scbond_it | 9.847 |
r_mcangle_it | 6.335 |
r_dihedral_angle_1_deg | 5.893 |
r_mcbond_it | 4.17 |
r_angle_refined_deg | 1.66 |
r_mcbond_other | 1.259 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1730 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 63 |
Software
Software | |
---|---|
Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DNA | data collection |
MOSFLM | data reduction |