Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, SO4, MOPSO and Butanetriol
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | Morpheus II-A1: Butanetriol 0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) and 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.11 | 60.46 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 139.779 | α = 90 |
| b = 139.779 | β = 90 |
| c = 274.11 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 2 2 |
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 | 2023-03-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.094 | 121.052 | 100 | 0.294 | 0.999 | 13.3 | 40.8 | 93328 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.094 | 2.13 | 100 | 0.315 | 0.5 | 42.2 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.094 | 50.459 | 1.33 | 92673 | 4583 | 99.31 | 0.1769 | 0.1751 | 0.1823 | 0.2106 | 0.2118 | ||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.362 |
| f_angle_d | 0.739 |
| f_chiral_restr | 0.047 |
| f_bond_d | 0.004 |
| f_plane_restr | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8078 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 712 |
| Heterogen Atoms | 160 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| autoPROC | data scaling |
| autoPROC | data reduction |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |














