3G0L
Crystal Structure of Human Bromodomain Adjacent to Zinc finger domain 2B (BAZ2B)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NXB | ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OO1 | ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OSS | ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2OUO | ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 2RFJ | ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
experimental model | PDB | 3DAI | ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 0.1M MMT pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.2 | 70.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.434 | α = 90 |
b = 96.314 | β = 90 |
c = 57.641 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | IMAGE PLATE | RIGAKU RAXIS IV | 2008-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5 |
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 | 2.03 | 23.62 | 96.4 | 0.079 | 0.079 | 12.5 | 3.7 | 15105 | 14561 | 31 |
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 | 2.03 | 2.14 | 94.4 | 0.606 | 0.606 | 2 | 3.7 | 2066 |
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 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI | 2.03 | 22.22 | 15201 | 14547 | 728 | 95.7 | 0.179 | 0.179 | 0.178 | 0.211 | RANDOM | 17.301 |
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] | |
2.01 | -0.99 | -1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.219 |
r_dihedral_angle_4_deg | 17.664 |
r_dihedral_angle_3_deg | 11.263 |
r_scangle_it | 8.573 |
r_scbond_it | 7.685 |
r_dihedral_angle_1_deg | 5.159 |
r_mcangle_it | 4.354 |
r_mcbond_it | 3.128 |
r_angle_refined_deg | 1.35 |
r_mcbond_other | 1.051 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 927 |
Nucleic Acid Atoms | |
Solvent Atoms | 134 |
Heterogen Atoms | 4 |
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 |