8I2A

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
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.741α = 90
b = 80.539β = 106.3
c = 77.258γ = 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
12.355099.50.1260.1510.0810.9973.430223
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)
12.352.4499.60.6140.7320.3950.7443.3

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 REPLACEMENTTHROUGHOUT5V0I2.355028710149599.330.215780.214290.24408RANDOM35.589
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]
-1.190.342.64-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.279
r_dihedral_angle_4_deg16.283
r_dihedral_angle_3_deg12.963
r_dihedral_angle_1_deg5.18
r_long_range_B_refined2.048
r_long_range_B_other2.048
r_mcangle_it1.159
r_mcangle_other1.158
r_angle_refined_deg1.102
r_angle_other_deg0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.279
r_dihedral_angle_4_deg16.283
r_dihedral_angle_3_deg12.963
r_dihedral_angle_1_deg5.18
r_long_range_B_refined2.048
r_long_range_B_other2.048
r_mcangle_it1.159
r_mcangle_other1.158
r_angle_refined_deg1.102
r_angle_other_deg0.87
r_scangle_other0.819
r_mcbond_it0.627
r_mcbond_other0.626
r_scbond_it0.432
r_scbond_other0.432
r_chiral_restr0.055
r_bond_refined_d0.007
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 Atoms5011
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms62

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction