4AQ7

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate analogue in the aminoacylation conformation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.533 MICROM LEURS, 50 MICROM TRNALEU AND 1 MM LEUCYL-ADENYLATE ANALOGUE MIXED EQUALLY WITH 0.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
1.942

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.66α = 90
b = 69.2β = 104.35
c = 228.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-11-29MSINGLE 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
12.55090.30.0811.12.975711
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)
12.52.676.60.522.12.16

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 1H3N2.539.6971885382690.330.190750.187520.25031RANDOM48.175
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]
0.18-0.07-0.620.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.966
r_dihedral_angle_4_deg20.381
r_dihedral_angle_3_deg19.305
r_dihedral_angle_1_deg7.282
r_angle_refined_deg1.77
r_angle_other_deg1.086
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.966
r_dihedral_angle_4_deg20.381
r_dihedral_angle_3_deg19.305
r_dihedral_angle_1_deg7.282
r_angle_refined_deg1.77
r_angle_other_deg1.086
r_chiral_restr0.094
r_bond_refined_d0.014
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 Atoms13670
Nucleic Acid Atoms3307
Solvent Atoms169
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing