2VL8
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP, CASTANOSPERMINE AND CALCIUM ION
X-RAY DIFFRACTION
Crystallization
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.95 | 57.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 57.689 | ¦Á = 90 |
| b = 191.332 | ¦Â = 90 |
| c = 205.384 | ¦Ã = 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 | 100 | CCD | MARRESEARCH | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | SLS | X06SA | |
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 | 2.31 | 95.78 | 99.6 | 0.16 | 11 | 8 | 100405 | 3 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.31 | 98.9 | 0.44 | 5.2 | 8 | ||||||||||||||
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 | OTHER | THROUGHOUT | 2.31 | 95.78 | 97392 | 3013 | 99.6 | 0.218 | 0.217 | 0.255 | RANDOM | 41.56 | |||||||
| 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] | |
| 0.41 | 0.91 | -1.32 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.664 |
| r_dihedral_angle_4_deg | 16.505 |
| r_dihedral_angle_3_deg | 15.354 |
| r_dihedral_angle_1_deg | 5.871 |
| r_scangle_it | 2.915 |
| r_scbond_it | 1.868 |
| r_angle_refined_deg | 1.372 |
| r_mcangle_it | 1.321 |
| r_mcbond_it | 0.773 |
| r_nbtor_refined | 0.303 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13201 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 400 |
| Heterogen Atoms | 119 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
