4TTE
Crystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 298 | 2.1-2.4M Ammonium Sulfate, 0.1M Bis-Tris pH5.5, 10% Glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.04 | 69.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.31 | α = 90 |
b = 79.31 | β = 90 |
c = 137.381 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | 193 | CCD | ADSC QUANTUM 315r | 2013-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11587 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.8 | 48.57 | 100 | 0.083 | 0.018 | 0.999 | 25 | 21.2 | 24459 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.8 | 1.84 | 100 | 0.98 | 0.28 | 0.804 | 2.5 | 13 | 1411 |
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 | 3DAI | 1.8 | 68.68 | 24396 | 1244 | 99.96 | 0.184 | 0.1833 | 0.197 | RANDOM | 30.077 |
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] | |
0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.521 |
r_dihedral_angle_4_deg | 14.334 |
r_dihedral_angle_3_deg | 13.296 |
r_dihedral_angle_1_deg | 4.329 |
r_mcangle_it | 2.975 |
r_mcbond_it | 1.954 |
r_mcbond_other | 1.946 |
r_angle_refined_deg | 1.482 |
r_angle_other_deg | 0.844 |
r_chiral_restr | 0.089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1084 |
Nucleic Acid Atoms | |
Solvent Atoms | 253 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |