3KT0

Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O5TPDB ENTRY 1O5T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M MES buffer, 0.05M CsCl, 30% v/v Jeffamine M-600 reagent, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4449.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.912α = 90
b = 55.912β = 90
c = 313.784γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2006-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon FactoryBL-6A

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
12.15096.60.1027.29.129469
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)
2.12.1898.50.5869.52911

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1O5T2.133.4529427147196.830.2080.2070.238RANDOM37.426
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]
1.881.88-3.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.777
r_dihedral_angle_3_deg14.258
r_dihedral_angle_4_deg12.437
r_sphericity_free10.112
r_dihedral_angle_1_deg5.283
r_scangle_it3.948
r_scbond_it2.486
r_mcangle_it1.95
r_rigid_bond_restr1.913
r_mcbond_it1.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.777
r_dihedral_angle_3_deg14.258
r_dihedral_angle_4_deg12.437
r_sphericity_free10.112
r_dihedral_angle_1_deg5.283
r_scangle_it3.948
r_scbond_it2.486
r_mcangle_it1.95
r_rigid_bond_restr1.913
r_mcbond_it1.456
r_sphericity_bonded1.157
r_angle_refined_deg1.075
r_nbtor_refined0.307
r_nbd_refined0.193
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.12
r_symmetry_hbond_refined0.086
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3025
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms14

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing