5XN7
Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | 6% 1,4 Dioxane, 0.1M MES pH6.5, 1.6M (NH4)2SO4 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.43 | 64.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 124.743 | α = 90 |
| b = 185.185 | β = 95.6 |
| c = 81.365 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 95 | PIXEL | DECTRIS PILATUS3 6M | 2015-10-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.97776 | SSRF | BL18U1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.69 | 103.12 | 99.9 | 0.127 | 0.137 | 0.052 | 3.7 | 6.8 | 50131 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.7 | 2.75 | 98.9 | 0.759 | 0.828 | 0.328 | 0.85 | 6 | |||||||||||
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 | SAD | THROUGHOUT | 2.7 | 50 | 47537 | 2554 | 99.51 | 0.20536 | 0.2033 | 0.24378 | RANDOM | 78.401 | |||||||
| 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] | |
| -3.67 | -0.51 | 7.71 | -4.14 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.011 |
| r_dihedral_angle_4_deg | 20.751 |
| r_dihedral_angle_3_deg | 18.758 |
| r_dihedral_angle_1_deg | 5.79 |
| r_angle_refined_deg | 1.311 |
| r_chiral_restr | 0.088 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | |
| r_angle_other_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8248 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 89 |
| Heterogen Atoms | 47 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data collection |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| PHENIX | phasing |
