3GBG
Crystal Structure of ToxT from Vibrio Cholerae O395
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000, 3.6-4.0% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.99 | 38.17 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 39.311 | α = 90 |
| b = 77.739 | β = 90 |
| c = 83.568 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 298 | CCD | ADSC QUANTUM 210 | Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing | 2008-03-10 | M | MAD | |||||
| 2 | 1 | x-ray | 298 | CCD | MARMOSAIC 300 mm CCD | Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry | 2007-12-13 | M | SINGLE WAVELENGTH | |||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.9789, 0.9184, 0.9184 | NSLS | X6A |
| 2 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.9785 | APS | 23-ID-B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | ||||||||
| 1,2 | 1.9 | 19.62 | 99.8 | 0.075 | 20831 | 20831 | 17.6 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1,2 | 1.9 | 2 | 100 | 0.41 | 0.244 | 5.21 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | MAD dataset | 1.9 | 19.62 | 20831 | 2051 | 99.8 | 0.214 | 0.214 | 0.245 | RANDOM | 37.5 | ||||||
| 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] | |
| 4.68 | 4.13 | -8.81 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 21.8 |
| c_mcangle_it | 4.2 |
| c_scangle_it | 3.51 |
| c_mcbond_it | 2.7 |
| c_scbond_it | 2.4 |
| c_angle_deg | 1.2 |
| c_improper_angle_d | 0.85 |
| c_bond_d | 0.01 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2125 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 217 |
| Heterogen Atoms | 18 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SOLVE | phasing |
| CNS | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
