4AS1

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and the benzoxaborole AN2679 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-AN2679 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 20 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ETHYLENE GLYCOL AS CRYOPROTECTANT
Crystal Properties
Matthews coefficientSolvent content
2.3647.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.68α = 90
b = 77.11β = 102.24
c = 91.14γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM Q1202007-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.025098.20.0714.23.6578307
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)
12.022.0984.50.691.62.81

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 1H3N2.0219.8574330397798.120.210070.207990.24922RANDOM43.17
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]
-0.11-0.45-0.02-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.3
r_dihedral_angle_4_deg19.24
r_dihedral_angle_3_deg15.918
r_dihedral_angle_1_deg6.365
r_angle_refined_deg1.641
r_angle_other_deg1.059
r_chiral_restr0.109
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.3
r_dihedral_angle_4_deg19.24
r_dihedral_angle_3_deg15.918
r_dihedral_angle_1_deg6.365
r_angle_refined_deg1.641
r_angle_other_deg1.059
r_chiral_restr0.109
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms6458
Nucleic Acid Atoms1786
Solvent Atoms402
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing