2BTE | pdb_00002bte

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H3NPDB ENTRY 1H3N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.55MG/ML LEUCYL-TRNA SYNTHETASE MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5 MM L-LEUCINE 15MM MGCL2 50MM MES PH6.5 0.8M AMMONIUM SULPHATE AGAINST RESERVOIR CONTAINING 1.5M AMMONIUM SULPHATE AND 0.1M MES PH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.968

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 204.121α = 90
b = 125.705β = 120.86
c = 175.432γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2003-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.92593.40.1112.535.557901283.6
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)
12.9351.20.33.142.36

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1H3N2.924.8978938236993.60.2170.2170.220.2530.24RANDOM82.2
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]
19.7433.88-16.1-3.64
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.6
c_scangle_it7.2
c_scbond_it4.53
c_mcangle_it2.29
c_mcbond_it1.31
c_angle_deg1.2
c_improper_angle_d1.18
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.6
c_scangle_it7.2
c_scbond_it4.53
c_mcangle_it2.29
c_mcbond_it1.31
c_angle_deg1.2
c_improper_angle_d1.18
c_bond_d0.008
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 Atoms14244
Nucleic Acid Atoms3352
Solvent Atoms18
Heterogen Atoms201

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing