3Q2E
Crystal structure of the second bromodomain of human bromodomain and WD repeat-containing protein 1 isoform A (WDR9)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3MB3 | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2OSS | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2OUO | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2GRC | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 2OO1 | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 3DAI | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 3D7C | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
experimental model | PDB | 3DWY | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 277 | 0.2M (NH4)COOCH3, 0.1M BisTris, 25% PEG 3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.66 | α = 90 |
b = 51.66 | β = 90 |
c = 151.36 | γ = 120 |
Symmetry | |
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Space Group | P 61 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 | 100 | CCD | ADSC QUANTUM 315 | 2010-11-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9700 | Diamond | I02 |
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 | 1.74 | 28.892 | 99.5 | 0.088 | 0.088 | 12.9 | 6.7 | 13033 | 12968 | 25.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.74 | 1.83 | 98 | 0.87 | 0.87 | 0.951 | 0.375 | 0.9 | 6.1 | 1797 |
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 | 3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY | 1.74 | 28.89 | 13042 | 12942 | 634 | 99.23 | 0.1867 | 0.1867 | 0.1852 | 0.2191 | RANDOM | 29.4449 |
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] | |
0.2 | 0.1 | 0.2 | -0.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.635 |
r_dihedral_angle_3_deg | 13.363 |
r_dihedral_angle_4_deg | 12.969 |
r_scangle_it | 10.535 |
r_scbond_it | 7.593 |
r_dihedral_angle_1_deg | 4.915 |
r_mcangle_it | 4.675 |
r_mcbond_it | 2.988 |
r_angle_refined_deg | 1.45 |
r_angle_other_deg | 0.934 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 862 |
Nucleic Acid Atoms | |
Solvent Atoms | 105 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DNA | data collection |
MOSFLM | data reduction |