8I2C

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. M HEPES pH 7.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.725α = 90
b = 80.43β = 106.05
c = 77.136γ = 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
12.075099.50.0690.0820.0440.99813.53.444074
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)
12.072.1399.50.5680.6720.3560.8413.5

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 REPLACEMENTTHROUGHOUT5V0I2.075041849220699.470.20230.200460.23755RANDOM34.952
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]
-2.230.792.4-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.266
r_dihedral_angle_4_deg14.805
r_dihedral_angle_3_deg12.862
r_dihedral_angle_1_deg5.294
r_long_range_B_refined3.752
r_long_range_B_other3.752
r_scangle_other2.368
r_mcangle_it2.079
r_mcangle_other2.078
r_scbond_it1.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.266
r_dihedral_angle_4_deg14.805
r_dihedral_angle_3_deg12.862
r_dihedral_angle_1_deg5.294
r_long_range_B_refined3.752
r_long_range_B_other3.752
r_scangle_other2.368
r_mcangle_it2.079
r_mcangle_other2.078
r_scbond_it1.459
r_scbond_other1.457
r_mcbond_it1.296
r_mcbond_other1.295
r_angle_refined_deg1.218
r_angle_other_deg0.897
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 Atoms5035
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction