Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 277 | ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.51 | 64.97 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 75.8 | α = 90 |
| b = 222.8 | β = 111.8 |
| c = 80.8 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 120 | IMAGE PLATE | M | SINGLE WAVELENGTH | ||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.6 | 11.5 | 3.7 | 2.3 | 45.7 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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) | R-Free Selection Details | Mean Isotropic B | |||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | T. thermophilus AspRS | 2.6 | 11.5 | 2 | 63304 | 3084 | 84.1 | 0.204 | 0.204 | 0.21 | 0.257 | 0.26 | RANDOM | 46.3 | |||
| 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] | |
| 5.06 | 4.7 | -7.6 | 2.54 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 26.6 |
| c_scangle_it | 6.3 |
| c_mcangle_it | 4.8 |
| c_scbond_it | 4.58 |
| c_mcbond_it | 3.21 |
| c_angle_deg | 1.5 |
| c_improper_angle_d | 1.16 |
| c_bond_d | 0.007 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9182 |
| Nucleic Acid Atoms | 3097 |
| Solvent Atoms | 402 |
| Heterogen Atoms | 72 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ALMN | model building |
| TSFGEN | model building |
| CNS | refinement |
| CCP4 | phasing |
| TSFGEN) | phasing |
