4TQ8
Dual binding mode for 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid binding to Human transthyretin (TTR)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.7 | 293 | Protein: 5 mg/ml 1 milli-M ligand Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) 40% (24% MPEG-5K, 0.1 M sodium acetate, pH 5.5) Drops: 1 micro-L protein-ligand complex 1 micro-L precipitant. Cryoprotectant:: 40% (12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % DMSO + 12.5 % 1,4-dioxane), 25% MPEG 5K, 0.1 M sodium propionate, sodium cacodylate, Bis-Tris-propane(65% component A pH 4; 35% B pH 9.5 and 1 milli-M ligand. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.14 | α = 90 |
b = 86.04 | β = 90 |
c = 63.48 | 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 | PIXEL | DECTRIS PILATUS 2M-F | 2014-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8729 | ESRF | ID23-2 |
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 | 1.52 | 43.1 | 99.8 | 0.145 | 0.137 | 11.9 | 8.73 | 37141 | 37078 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.52 | 1.61 | 98.8 | 1.01 | 7.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | FOURIER SYNTHESIS | THROUGHOUT | 1.52 | 38.56 | 35223 | 1854 | 99.84 | 0.18728 | 0.18605 | 0.2098 | RANDOM | 22.219 |
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] | |
0.51 | -0.54 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.192 |
r_dihedral_angle_3_deg | 14.879 |
r_dihedral_angle_4_deg | 13.451 |
r_dihedral_angle_1_deg | 6.064 |
r_angle_refined_deg | 2.112 |
r_chiral_restr | 0.15 |
r_bond_refined_d | 0.022 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1794 |
Nucleic Acid Atoms | |
Solvent Atoms | 232 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
XDS | data scaling |
MOLREP | phasing |
MxCuBE | data collection |