3GWS
Crystal Structure of T3-Bound Thyroid Hormone Receptor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2H6W | PDB entry 2H6W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 298 | 100MM SODIUM CACODYLATE, 1.4M SODIUM ACETATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.974 | α = 90 |
b = 68.974 | β = 90 |
c = 131.247 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | MAR scanner 345 mm plate | MIRRORS | 2004-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU ULTRAX 18 | 1.5478 |
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 | 2.2 | 24.667 | 96.2 | 0.067 | 0.067 | 16.9 | 6.3 | 18952 | 18232 | 2 | 2 | 42.844 |
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) | ||||||||||
2.2 | 2.32 | 95.2 | 0.618 | 0.618 | 2.5 | 6.1 | 2583 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | PDB entry 2H6W | 2.2 | 24.667 | 0.03 | 35459 | 29016 | 1471 | 81.83 | 0.193 | 0.1909 | 0.233 | RANDOM |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.03 |
f_angle_deg | 0.709 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1934 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
MOLREP | phasing |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |