3ZJT

Ternary complex of E.coli leucyl-tRNA synthetase, tRNA(Leu)574 and the benzoxaborole AN3017 in the editing conformation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6THE TERNARY COMPLEX ECLEURS-TRNA-AN3017 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE AT PH 5.6, 14-18 % PEG 6000 AND 200 MM NACL. CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING A CRYOPROTECTING SOLUTION CONTAINING 22 % ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.5556.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.9α = 90
b = 118.8β = 90
c = 140.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-12-06MSINGLE 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
12.290.599.70.0713.73.9965794
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)
12.22.2599.80.462.93.97

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1H3N2.290.5462461333399.70.209060.206820.2506RANDOM44.762
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]
-0.720.470.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.847
r_dihedral_angle_4_deg19.035
r_dihedral_angle_3_deg17.104
r_dihedral_angle_1_deg7.167
r_angle_refined_deg1.361
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.847
r_dihedral_angle_4_deg19.035
r_dihedral_angle_3_deg17.104
r_dihedral_angle_1_deg7.167
r_angle_refined_deg1.361
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6517
Nucleic Acid Atoms1767
Solvent Atoms274
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing