3SZ3

Crystal structure of Tryptophanyl-tRNA synthetase from Vibrio cholerae with an endogenous tryptophan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N9I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION760% Tascimate, pH 7, vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.02α = 90
b = 94.047β = 90
c = 47.036γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2010-11-11SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97903APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.54099.60.04119.26.754037
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5398.50.4035.92646

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 REPLACEMENTTHROUGHOUT3N9I1.526.0953996274599.170.16060.15960.179RANDOM22.8065
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]
-0.82-0.261.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg18.368
r_dihedral_angle_3_deg12.268
r_dihedral_angle_1_deg5.426
r_scangle_it3.372
r_scbond_it2.105
r_angle_refined_deg1.458
r_mcangle_it1.407
r_angle_other_deg0.909
r_mcbond_it0.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg18.368
r_dihedral_angle_3_deg12.268
r_dihedral_angle_1_deg5.426
r_scangle_it3.372
r_scbond_it2.105
r_angle_refined_deg1.458
r_mcangle_it1.407
r_angle_other_deg0.909
r_mcbond_it0.806
r_mcbond_other0.216
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2621
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing