8I4I

The asymmetric structure of homodimeric E. coli TrpRS bound with tryptophanyl adenylate and L-tryptophan


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
2.3948.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.664α = 90
b = 80.048β = 106.2
c = 77.435γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELRIGAKU HyPix-6000HE2022-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.25099.90.1310.0550.99312.75.436816
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.321000.5560.2780.8263.8

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 REPLACEMENTTHROUGHOUT5V0I2.25034885191799.880.207970.206790.229RANDOM21.006
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]
-1.520.171.92-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.203
r_dihedral_angle_4_deg15.005
r_dihedral_angle_3_deg11.922
r_dihedral_angle_1_deg5.096
r_long_range_B_other1.735
r_long_range_B_refined1.734
r_angle_refined_deg1.11
r_angle_other_deg0.873
r_mcangle_it0.766
r_mcangle_other0.766
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.203
r_dihedral_angle_4_deg15.005
r_dihedral_angle_3_deg11.922
r_dihedral_angle_1_deg5.096
r_long_range_B_other1.735
r_long_range_B_refined1.734
r_angle_refined_deg1.11
r_angle_other_deg0.873
r_mcangle_it0.766
r_mcangle_other0.766
r_scangle_other0.527
r_mcbond_it0.413
r_mcbond_other0.413
r_scbond_it0.277
r_scbond_other0.277
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms5015
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CrysalisProdata reduction