6IJF
Crystal structure of the type VI effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4BI8 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 35 % PEG 400, 0.05 M Tris pH 8.5, 0.05 M sodium sulfate, 0.05 M lithium sulfate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.46 | 49.96 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.025 | α = 90 |
| b = 72.025 | β = 90 |
| c = 194.348 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 |
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 | RAYONIX MX225-HS | 2015-12-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.0000 | SPring-8 | BL32XU |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.9 | 97.18 | 99.6 | 0.067 | 0.07 | 0.022 | 0.999 | 15 | 10.1 | 44633 | |||||||||
| 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 | 1.9 | 1.94 | 96.3 | 1.431 | 1.538 | 0.544 | 0.528 | 7.3 | |||||||||||
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 | 4BI8 | 1.9 | 62.38 | 42275 | 2278 | 99.54 | 0.19142 | 0.19027 | 0.21252 | RANDOM | 47.589 | ||||||
| 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] | |
| 0.95 | 0.47 | 0.95 | -3.08 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.819 |
| r_dihedral_angle_1_deg | 20.979 |
| r_dihedral_angle_4_deg | 18.281 |
| r_dihedral_angle_3_deg | 15.66 |
| r_long_range_B_other | 9.235 |
| r_long_range_B_refined | 9.229 |
| r_scangle_other | 6.79 |
| r_mcangle_other | 5.63 |
| r_mcangle_it | 5.629 |
| r_scbond_it | 4.908 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4036 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 122 |
| Heterogen Atoms | 21 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| DIALS | data reduction |
| MOLREP | phasing |
