8I1Y

The structure of E. coli TrpRS bound with a chemical fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V0I 

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
2.4349.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.69α = 90
b = 79.97β = 105.79
c = 78.54γ = 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
11.785099.80.050.0550.0220.99918.4670259
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)
11.781.8298.60.6460.7440.3610.8524.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.785066833340499.80.191480.189820.22428RANDOM29.447
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]
-2.850.343.47-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.232
r_dihedral_angle_4_deg16.071
r_dihedral_angle_3_deg11.286
r_dihedral_angle_1_deg5.67
r_long_range_B_refined3.857
r_long_range_B_other3.683
r_scangle_other2.395
r_mcangle_it1.912
r_mcangle_other1.909
r_scbond_it1.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.232
r_dihedral_angle_4_deg16.071
r_dihedral_angle_3_deg11.286
r_dihedral_angle_1_deg5.67
r_long_range_B_refined3.857
r_long_range_B_other3.683
r_scangle_other2.395
r_mcangle_it1.912
r_mcangle_other1.909
r_scbond_it1.514
r_scbond_other1.506
r_angle_other_deg1.415
r_mcbond_it1.233
r_mcbond_other1.233
r_angle_refined_deg1.217
r_chiral_restr0.064
r_gen_planes_refined0.005
r_bond_refined_d0.004
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 Atoms5087
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms72

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction
MOLREPphasing