5ON2

Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline 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
2.4850.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.65α = 90
b = 70.62β = 104.52
c = 230.34γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
13.15099.60.010.996.13.345457
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)
13.13.2199.910.291.13.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4AQ73.15043264219399.620.227570.225780.26316RANDOM95.831
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]
-0.25-1.330.180.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.872
r_dihedral_angle_3_deg12.19
r_dihedral_angle_4_deg11.608
r_dihedral_angle_1_deg4.99
r_long_range_B_refined4.31
r_long_range_B_other4.31
r_mcangle_it2.847
r_mcangle_other2.847
r_scangle_other2.079
r_mcbond_it1.552
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.872
r_dihedral_angle_3_deg12.19
r_dihedral_angle_4_deg11.608
r_dihedral_angle_1_deg4.99
r_long_range_B_refined4.31
r_long_range_B_other4.31
r_mcangle_it2.847
r_mcangle_other2.847
r_scangle_other2.079
r_mcbond_it1.552
r_mcbond_other1.552
r_scbond_it1.145
r_scbond_other1.145
r_angle_refined_deg0.907
r_angle_other_deg0.899
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 Atoms13676
Nucleic Acid Atoms3538
Solvent Atoms
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing