3ESP
Human transthyretin (TTR) complexed with N-(3,5-Dibromo-4-hydroxyphenyl)-3,5-dimethyl-4-hydroxybenzamide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 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 with inhibitors 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 | |
---|---|
Matthews coefficient | Solvent content |
2.12 | 41.97 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 42.583 | α = 90 |
b = 85.337 | β = 90 |
c = 64.284 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing) | 2007-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.9795 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.31 | 64.28 | 96.4 | 0.04 | 36.6 | 6.5 | 55178 | 17.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1.31 | 1.36 | 75.1 | 0.331 | 3.6 | 4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | 1.31 | 50 | 55131 | 2794 | 96.74 | 0.178 | 0.177 | 0.201 | RANDOM | 19.831 |
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] | |
0.3 | 0.43 | -0.72 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.438 |
r_dihedral_angle_4_deg | 18.978 |
r_dihedral_angle_3_deg | 13.42 |
r_sphericity_free | 10.208 |
r_sphericity_bonded | 7.485 |
r_scangle_it | 6.207 |
r_dihedral_angle_1_deg | 6.011 |
r_scbond_it | 4.171 |
r_mcangle_it | 3.212 |
r_mcbond_it | 2.122 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1892 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 42 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |