8I27

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
2.448.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.717α = 90
b = 80.588β = 106.22
c = 77.159γ = 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
11.955097.30.0570.0680.0360.99712.93.451416
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)
11.95291.80.4230.5070.2760.8893.1

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 REPLACEMENTTHROUGHOUT5V0I1.955048799259796.990.192170.19040.22545RANDOM29.269
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]
-1.590.441.95-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.996
r_dihedral_angle_4_deg16.583
r_dihedral_angle_3_deg11.863
r_dihedral_angle_1_deg5.125
r_long_range_B_refined3.385
r_long_range_B_other3.385
r_scangle_other1.992
r_mcangle_it1.681
r_mcangle_other1.681
r_scbond_it1.203
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.996
r_dihedral_angle_4_deg16.583
r_dihedral_angle_3_deg11.863
r_dihedral_angle_1_deg5.125
r_long_range_B_refined3.385
r_long_range_B_other3.385
r_scangle_other1.992
r_mcangle_it1.681
r_mcangle_other1.681
r_scbond_it1.203
r_scbond_other1.202
r_angle_refined_deg1.157
r_mcbond_it1.019
r_mcbond_other1.018
r_angle_other_deg0.878
r_chiral_restr0.062
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 Atoms5041
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms56

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction