8OU8

Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QF6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.929312% (w/v) PEG 4000, 21% (v/v) MPD, and 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.76313155

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.33α = 90
b = 108.95β = 90
c = 113.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2022-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0578.75990.9949.32.245827
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.258480.996

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0578.7543429239768.150.2160.188920.266RANDOM41.717
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]
-0.50.180.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.056
r_dihedral_angle_3_deg17.127
r_long_range_B_refined8.625
r_long_range_B_other8.589
r_dihedral_angle_1_deg7.775
r_scangle_other6.424
r_mcangle_it4.927
r_mcangle_other4.926
r_scbond_it4.419
r_scbond_other4.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.056
r_dihedral_angle_3_deg17.127
r_long_range_B_refined8.625
r_long_range_B_other8.589
r_dihedral_angle_1_deg7.775
r_scangle_other6.424
r_mcangle_it4.927
r_mcangle_other4.926
r_scbond_it4.419
r_scbond_other4.418
r_mcbond_it3.511
r_mcbond_other3.511
r_angle_refined_deg1.563
r_angle_other_deg0.522
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms6560
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms39

Software

Software
Software NamePurpose
autoPROCdata processing
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement