4MAS
High Resolution Structure of Wild Type Human Transthyretin in Complex with 3,3',5,5'-tetrachloro-[1,1'-biphenyl]-4,4'diol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FBR | PDB ENTRY 2FBR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | 4 mg/ML wt-TTR in 10 mM sodium phosphate, 100 mM potassium chloride, pH 7.6, co-crystallized with inhibitor, crystallization solution: 1.395 M sodium citrate, 3.5% v/v glycerol, pH 5.5, cryoprotectant: 1.395 M sodium citrate, pH 5.5, 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.049 | α = 90 |
b = 85.02 | β = 90 |
c = 64.893 | 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 | 200 | PIXEL | DECTRIS PILATUS 6M | Rh coated flat mirror | 2013-07-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.9797 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.22 | 35.873 | 99.5 | 0.028 | 27.6 | 6.3 | 70897 | 13.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.22 | 1.29 | 98.2 | 0.515 | 3.5 | 6 | 10085 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2FBR | 1.22 | 35.873 | 67215 | 3580 | 99.25 | 0.15168 | 0.15053 | 0.17339 | RANDOM | 17.368 |
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] | |
-0.04 | -0.02 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.931 |
r_sphericity_free | 30.197 |
r_dihedral_angle_4_deg | 18.792 |
r_sphericity_bonded | 13.687 |
r_dihedral_angle_3_deg | 11.602 |
r_dihedral_angle_1_deg | 6.292 |
r_rigid_bond_restr | 4.684 |
r_angle_refined_deg | 1.649 |
r_angle_other_deg | 0.952 |
r_chiral_restr | 0.1 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1782 |
Nucleic Acid Atoms | |
Solvent Atoms | 179 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
autoXDS | data collection |
PHASER | phasing |
REFMAC | refinement |
autoXDS | data reduction |
autoXDS | data scaling |