1H3E

Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with wild-type tRNAtyr(GUA) and with ATP and tyrosinol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherT. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY DETERMINED BY SIRAS BY SAME AUTHORS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17DROP: 5MG/ML TYRRSTT+TRNA(TYR)WITH 5MM TYROSINOL, 10MM MGCL2, 10MM ATP, 50MM HEPES (PH7.0), 0.8M AMMONIUM SULPHATE. RESERVOIR: 1.5-1.6M AMMONIUM SULPHATE, 100MM HEPES (PH7.0)., pH 7.00
Crystal Properties
Matthews coefficientSolvent content
3.6365.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.525α = 90
b = 129.525β = 90
c = 109.451γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2001-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.92394.90.0755.93.422669115.5
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)
12.92.9863.80.5091.51.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTT. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY DETERMINED BY SIRAS BY SAME AUTHORS2.922.9922644114994.90.2190.2190.269RANDOM77.3
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]
10.0622.2210.06-20.13
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.9
c_scangle_it8.15
c_scbond_it5.35
c_mcangle_it2.09
c_angle_deg1.3
c_improper_angle_d1.26
c_mcbond_it1.21
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.9
c_scangle_it8.15
c_scbond_it5.35
c_mcangle_it2.09
c_angle_deg1.3
c_improper_angle_d1.26
c_mcbond_it1.21
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3403
Nucleic Acid Atoms1762
Solvent Atoms13
Heterogen Atoms43

Software

Software
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing