3IMR
Transthyretin in complex with (E)-2,6-dibromo-4-(2,6-dichlorostyryl)phenol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QGB | pdb entry 2QGB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.927 | α = 90 |
b = 85.002 | β = 90 |
c = 64.506 | 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 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, double crystal monochromator, toroid focusing mirror | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.9194 | SSRL | BL9-2 |
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 | 1.7 | 64.55 | 99.5 | 0.057 | 34.6 | 14 | 26903 | 23.6 |
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) | |||||||||||
1.7 | 1.76 | 97 | 0.695 | 7.3 | 11.9 | 2588 |
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 2QGB | 1.7 | 50 | 26562 | 1333 | 99.56 | 0.172 | 0.169 | 0.217 | RANDOM | 27.504 |
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] | |
1.18 | -0.72 | -0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.117 |
r_dihedral_angle_4_deg | 17.51 |
r_dihedral_angle_3_deg | 14.69 |
r_sphericity_free | 10.749 |
r_dihedral_angle_1_deg | 5.988 |
r_scangle_it | 5.86 |
r_sphericity_bonded | 5.544 |
r_rigid_bond_restr | 5.136 |
r_scbond_it | 4.646 |
r_mcangle_it | 3.06 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1863 |
Nucleic Acid Atoms | |
Solvent Atoms | 85 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |