6HHW

Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)uridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L0W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were grown by mixing an equal volume of the protein solution with 8-12% PEG 4000, 0.1 M Morpheus buffer system 1 (MES/imidazole) pH 7, 100 mM KCl, 20 v/v % glycerol. For soaking a 4 mM solution of compound in DMSO was used. A one third volume of the initial drop size was pipetted carefully onto the crystal containing drop. The sample was then placed back over the reservoir and incubated for approximately 2 hr. Crystals we caught in cryoloops and directly flash frozen in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
2.9558.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.755α = 90
b = 112.887β = 104.92
c = 87.529γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.96863ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.087999.80.0520.060.0310.99911.43.89149249.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.299.90.7120.830.4220.7343.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1L0W2.2790.3177679201899.750.18670.18580.222165.0081
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8987
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms58

Software

Software
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing