3LXJ
Crystal Structure of the Bromodomain of Human AAA domain containing 2B (ATAD2B)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DAI | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 2NXB | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 2OO1 | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 2OSS | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 2OUO | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 2RFJ | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 3HMH | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 3D7C | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
experimental model | PDB | 3DWY | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 20% isopropanol 0.1M tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.64 | α = 90 |
b = 79.64 | β = 90 |
c = 204.051 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 2009-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9204 | Diamond | I04 |
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 | 2.327 | 40.81 | 99.3 | 0.08 | 0.08 | 10.8 | 4.9 | 31225 | 31006 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.34 | 2.46 | 99.6 | 0.653 | 0.653 | 2 | 4.4 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | ensemble of 3DAI, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3HMH, 3D7C, 3DWY | 2.33 | 40.81 | 31012 | 29113 | 1586 | 98.99 | 0.21405 | 0.21206 | 0.2534 | RANDOM | 45.949 |
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] | |
6.62 | 6.62 | -13.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.432 |
r_dihedral_angle_3_deg | 15.461 |
r_dihedral_angle_4_deg | 15.132 |
r_scangle_it | 6.558 |
r_scbond_it | 6.334 |
r_dihedral_angle_1_deg | 5.799 |
r_mcangle_it | 3.906 |
r_mcbond_it | 2.856 |
r_angle_refined_deg | 1.307 |
r_mcbond_other | 1.21 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4268 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
MOSFLM | data reduction |