3N9I

Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FI0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72910.2 M Ca(oAc)2 0.1 M Tris 20% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.099α = 90
b = 78.15β = 90
c = 152.176γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2010-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
11.954099.20.0779.35.4557455329022
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)
11.951.9898.40.652.85.32581

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3FI01.9540225304050347269398.660.180.169050.167070.20615RANDOM22.724
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]
-0.280.75-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.311
r_dihedral_angle_4_deg18.84
r_dihedral_angle_3_deg13.712
r_dihedral_angle_1_deg5.276
r_scangle_it4.459
r_scbond_it2.691
r_mcangle_it1.661
r_angle_refined_deg1.42
r_angle_other_deg0.907
r_mcbond_it0.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.311
r_dihedral_angle_4_deg18.84
r_dihedral_angle_3_deg13.712
r_dihedral_angle_1_deg5.276
r_scangle_it4.459
r_scbond_it2.691
r_mcangle_it1.661
r_angle_refined_deg1.42
r_angle_other_deg0.907
r_mcbond_it0.893
r_mcbond_other0.235
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5209
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms7

Software

Software
Software NamePurpose
SBC-Collectdata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling