8I1W

The asymmetric structure of homodimeric E. coli TrpRS bound with tryptophanyl adenylate at one of its two active pockets


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
2.3948.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.68α = 90
b = 79.68β = 106.04
c = 77.65γ = 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
11.85098.80.0610.0670.0270.99818.26.565978
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)
11.81.8498.30.4830.5230.1990.9716.9

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 REPLACEMENTTHROUGHOUT1.85062587337298.510.187720.185940.22171RANDOM30.285
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]
-3.340.851.051.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.467
r_dihedral_angle_4_deg15.611
r_dihedral_angle_3_deg11.615
r_dihedral_angle_1_deg5.228
r_long_range_B_refined3.236
r_long_range_B_other3.103
r_scangle_other1.789
r_mcangle_it1.525
r_mcangle_other1.522
r_angle_refined_deg1.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.467
r_dihedral_angle_4_deg15.611
r_dihedral_angle_3_deg11.615
r_dihedral_angle_1_deg5.228
r_long_range_B_refined3.236
r_long_range_B_other3.103
r_scangle_other1.789
r_mcangle_it1.525
r_mcangle_other1.522
r_angle_refined_deg1.148
r_scbond_it1.074
r_scbond_other1.068
r_mcbond_it0.915
r_mcbond_other0.912
r_angle_other_deg0.867
r_chiral_restr0.062
r_bond_refined_d0.006
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 Atoms5094
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms57

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction
MOLREPphasing