4DEU
Crystal Structure of the Wild Type TTR Binding Naringenin (TTRwt:NAR)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.734 | α = 90 |
b = 85.173 | β = 90 |
c = 65.058 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | MARMOSAIC 225 mm CCD | 2009-04-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.46 | LNLS | W01B-MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.599 | 25 | 87 | 0.064 | 11.1 | 5.1 | 29385 | 29385 | 2 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.599 | 22.254 | 1.34 | 29385 | 29385 | 1507 | 89.48 | 0.1906 | 0.1893 | 0.2133 | 21.4597 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-5.3089 | 0.0131 | 5.2958 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.036 |
f_angle_d | 2.088 |
f_chiral_restr | 0.17 |
f_bond_d | 0.045 |
f_plane_restr | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1790 |
Nucleic Acid Atoms | |
Solvent Atoms | 218 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
HKL-2000 | data reduction |
PHASER | phasing |