5ON3 | pdb_00005on3

Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AQ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.3748.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159α = 90
b = 68.7β = 102.8
c = 227.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
13.15098.60.020.975.23.543333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2398.510.391.13.2

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 REPLACEMENTTHROUGHOUT4AQ73.1221.5541189214498.580.242930.241130.240.277530.28RANDOM70.008
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]
-0.99-1.323.85-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.193
r_dihedral_angle_3_deg11.729
r_dihedral_angle_4_deg10.127
r_dihedral_angle_1_deg4.919
r_long_range_B_refined2.847
r_long_range_B_other2.847
r_mcangle_it1.777
r_mcangle_other1.777
r_scangle_other1.297
r_mcbond_it0.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.193
r_dihedral_angle_3_deg11.729
r_dihedral_angle_4_deg10.127
r_dihedral_angle_1_deg4.919
r_long_range_B_refined2.847
r_long_range_B_other2.847
r_mcangle_it1.777
r_mcangle_other1.777
r_scangle_other1.297
r_mcbond_it0.955
r_mcbond_other0.955
r_angle_refined_deg0.895
r_angle_other_deg0.886
r_scbond_it0.71
r_scbond_other0.71
r_chiral_restr0.053
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13594
Nucleic Acid Atoms3350
Solvent Atoms
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing