3ADB
Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 1)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 293 | 14.5% PEG 3350, 40mM sodium citrate-HCl (pH 5.2), 260mM ammonium tartrate, 5.0mM magnesium chloride, 1.0mM AMPPNP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.25 | 45.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 92.196 | α = 90 |
| b = 260.923 | β = 90 |
| c = 45.558 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 90 | CCD | RAYONIX MX225HE | monochromator | 2009-05-26 | M | SINGLE WAVELENGTH | |||||
| 2 | 1 | x-ray | 90 | CCD | ADSC QUANTUM 210 | 2009-04-26 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.000 | SPring-8 | BL41XU |
| 2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 0.97904, 0.97931, 0.96408 | Photon Factory | AR-NW12A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.8 | 50 | 99.9 | 0.15 | 0.15 | 14.8 | 7.3 | 28439 | 28411 | -3 | 88.8 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 2.8 | 2.9 | 100 | 0.66 | 0.66 | 3.01 | 7.4 | 2779 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MAD | THROUGHOUT | 2.8 | 40.84 | 28112 | 28071 | 1421 | 99.9 | 0.23 | 0.228 | 0.269 | RANDOM | 46 | ||||||
| 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] | |
| -1.1 | 16.26 | -15.15 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 16.4 |
| c_scangle_it | 4.99 |
| c_mcangle_it | 4.02 |
| c_scbond_it | 3.61 |
| c_mcbond_it | 2.83 |
| c_improper_angle_d | 1.16 |
| c_angle_deg | 1.1 |
| 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 | 4174 |
| Nucleic Acid Atoms | 3936 |
| Solvent Atoms | 159 |
| Heterogen Atoms | 37 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| autoSHARP | phasing |
| CNS | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
