8I1Z

E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment


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
2.4449.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.79α = 90
b = 80.15β = 105.77
c = 78.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.9792SSRFBL02U1

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
11.850.0199.20.0530.0640.0350.99711.6367909
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)
11.81.8498.70.3740.4850.3060.882.2

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 REPLACEMENTTHROUGHOUT5V0I1.850.0164433345499.070.196690.195010.22855RANDOM34.245
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]
-2.840.643.4-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.68
r_dihedral_angle_4_deg17.573
r_dihedral_angle_3_deg11.68
r_dihedral_angle_1_deg5.231
r_long_range_B_refined3.658
r_long_range_B_other3.58
r_scangle_other2.328
r_mcangle_it1.879
r_mcangle_other1.876
r_scbond_it1.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.68
r_dihedral_angle_4_deg17.573
r_dihedral_angle_3_deg11.68
r_dihedral_angle_1_deg5.231
r_long_range_B_refined3.658
r_long_range_B_other3.58
r_scangle_other2.328
r_mcangle_it1.879
r_mcangle_other1.876
r_scbond_it1.387
r_scbond_other1.387
r_mcbond_it1.162
r_mcbond_other1.162
r_angle_refined_deg1.159
r_angle_other_deg0.88
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms5109
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms64

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction