6OD8
Crystal structure of a putative aspartyl-tRNA synthetase from Leishmania major Friedlin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Microlytic MCSG-1 screen G9: 20% (w/V) PEG 3350, 200mM sodium formate: LemaA.00612.a.B1.PW38547 at 21.8mg/ml: cryo: 20% EG in two steps: tray 306454 G9: puck xyn7-2. For experimental phasing, a crystal from the same well was incubated for 10sec each in a solution of a) 90% reservoir and 10% 2.5M Sodium iodide in ethylene glycol and a solution of b) a) 80% reservoir and 20% 2.5M Sodium iodide in ethylene glycol a s and vitrified: puck: bbh6-4. Well diffracting monoclinic crystals with a larger unit cell and four copies of the protein in the ASU also grew under condition MCSG-1 D9: 25% (w/V) PEG 3350, 200mM NaCl, 100mM Tris pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.01 | α = 90 |
b = 142.36 | β = 97.2 |
c = 68.28 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2019-03-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.85 | 46.111 | 99 | 0.061 | 0.064 | 0.999 | 20.88 | 8.76 | 97249 | 29.613 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.85 | 1.9 | 92.1 | 0.334 | 0.4 | 0.872 | 2.87 | 3.109 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.85 | 46.111 | 1.36 | 97236 | 1892 | 99.01 | 0.1574 | 0.1567 | 0.1919 | 0 | 29.6474 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7927 |
Nucleic Acid Atoms | |
Solvent Atoms | 820 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Coot | model building |
ARP/wARP | model building |