8I2L

E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment at the dimerization interface


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2900.16M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4249.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.617α = 90
b = 80.047β = 105.69
c = 78.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9785SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.955099.40.0660.0790.0430.99710.93.353051
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95297.50.3740.4540.2550.9362.9

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 REPLACEMENTTHROUGHOUT5V0I1.955050390263699.240.200330.199260.22146RANDOM33.751
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]
-3.460.322.70.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.56
r_dihedral_angle_4_deg20.231
r_dihedral_angle_3_deg12.076
r_dihedral_angle_1_deg5.309
r_long_range_B_refined3.702
r_long_range_B_other3.702
r_scangle_other2.287
r_mcangle_it2.007
r_mcangle_other2.007
r_scbond_it1.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.56
r_dihedral_angle_4_deg20.231
r_dihedral_angle_3_deg12.076
r_dihedral_angle_1_deg5.309
r_long_range_B_refined3.702
r_long_range_B_other3.702
r_scangle_other2.287
r_mcangle_it2.007
r_mcangle_other2.007
r_scbond_it1.359
r_scbond_other1.359
r_mcbond_it1.222
r_mcbond_other1.219
r_angle_refined_deg1.198
r_angle_other_deg0.899
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms5068
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction