5F5W

Crystal structure of the alpha subunit of glycyl tRNA synthetase (GlyRS) from Aquifex aeolicus in complex with an analog of glycyl adenylate (Gly-SA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J5W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15Drops containing 1 microliter of alpha-AaGlyRS at 15 mg/ml yielded crystals at 18C when mixed with 1 microliter of a reservoir solution containing 30% polyethylene glycol monomethyl ether 2000 and 100 mM potassium thiocyanate. Crystals were soaked for 2 days in a solution containing a final concentration of 28 mM GSAd by mixing 1.3 microliters of the drop containing crystals, 2.5 microliters of reservoir solution and 1.5 microliters of GSAd at 100 mM
Crystal Properties
Matthews coefficientSolvent content
2.7257

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.829α = 90
b = 130.01β = 90
c = 145.52γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9785APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.8183.431000.0849.74.4478244782455
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.812.911000.5842.24.5

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1J5W2.8180.1661.3447741240999.920.23960.23890.2521random selection
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.336
f_angle_d1.462
f_chiral_restr0.098
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11740
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms135

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOSFLMdata reduction
BALBESphasing
Cootmodel building