Crystal Structure of Mu class Glutathione-S-Transferase TuGSTm06(Tetur05g05220) in complex with reaction product
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8UDE | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 2.4 M sodium malonate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.4 | 63.78 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 133.473 | α = 90 |
| b = 133.473 | β = 90 |
| c = 103.738 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2022-04-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.000 | APS | 22-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.05 | 40 | 96.2 | 0.061 | 0.398 | 0.99 | 20.2 | 2.3 | 41596 | -3 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.05 | 2.09 | 94.7 | 0.607 | 0.396 | 0.733 | 1.5 | 2.1 | |||||||||||
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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.05 | 34.603 | 41594 | 2003 | 96.184 | 0.173 | 0.1719 | 0.1804 | 0.1927 | 0.2032 | 42.811 | ||||||
| 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] | |
| -0.952 | -0.476 | -0.952 | 3.088 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 14.541 |
| r_dihedral_angle_3_deg | 13.481 |
| r_dihedral_angle_6_deg | 12.404 |
| r_lrange_it | 8.601 |
| r_lrange_other | 8.578 |
| r_scangle_it | 6.451 |
| r_scangle_other | 6.45 |
| r_dihedral_angle_1_deg | 4.813 |
| r_scbond_other | 4.461 |
| r_scbond_it | 4.458 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3643 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 301 |
| Heterogen Atoms | 148 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| MOLREP | phasing |
