4QY4
Crystal structure of the bromodomain of human SMARCA2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GRC | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
experimental model | PDB | 2OSS | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
experimental model | PDB | 3D7C | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
experimental model | PDB | 2OUO | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
experimental model | PDB | 2OO1 | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
experimental model | PDB | 3DAI | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
experimental model | PDB | 3DWY | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 15% PEG 6K, 8% ethylene glycol, 0.01M ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.18 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 64.346 | ¦Á = 90 |
b = 64.346 | ¦Â = 90 |
c = 89.117 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 |
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 6M | 2014-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97630 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.97 | 55.73 | 100 | 0.219 | 0.141 | 11.9 | 6.6 | 28970 | 28970 | 18.046 |
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 | 1.99 | 2.04 | 100 | 3.29 | 1.324 | 2.8 | 6 | 10355 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY. | 1.97 | 55.73 | 28970 | 27508 | 1415 | 98.75 | 0.22633 | 0.22633 | 0.22367 | 0.27889 | RANDOM | 36.384 |
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] | |
0.73 | 0.36 | 0.73 | -2.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.008 |
r_dihedral_angle_4_deg | 16.889 |
r_dihedral_angle_3_deg | 15.297 |
r_dihedral_angle_1_deg | 5.866 |
r_long_range_B_refined | 5.054 |
r_long_range_B_other | 5.01 |
r_scangle_other | 3.162 |
r_mcangle_it | 2.262 |
r_mcangle_other | 2.262 |
r_scbond_it | 1.941 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2650 |
Nucleic Acid Atoms | |
Solvent Atoms | 98 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |