2G36

Crystal structure of Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan-tRNA ligase)(TrpRS) (tm0492) from THERMOTOGA MARITIMA at 2.50 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP6.527712.5% PEG-3000, 0.25M MgCl2, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
3.3763.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.89α = 90
b = 152.73β = 90
c = 53.07γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.00ALS8.2.2

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
12.529.6491.40.0788.821.931763649.406
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)
12.52.5997.982.40.472.11.86

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1yi8B2.529.641762389499.280.1970.197240.1940.256RANDOM35.567
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]
2.09-1.52-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.224
r_dihedral_angle_4_deg14.102
r_dihedral_angle_3_deg11.769
r_scangle_it6.681
r_scbond_it4.903
r_dihedral_angle_1_deg3.256
r_mcangle_it2.751
r_mcbond_it1.704
r_angle_refined_deg1.603
r_angle_other_deg1.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.224
r_dihedral_angle_4_deg14.102
r_dihedral_angle_3_deg11.769
r_scangle_it6.681
r_scbond_it4.903
r_dihedral_angle_1_deg3.256
r_mcangle_it2.751
r_mcbond_it1.704
r_angle_refined_deg1.603
r_angle_other_deg1.012
r_mcbond_other0.328
r_symmetry_vdw_refined0.282
r_nbd_refined0.226
r_nbd_other0.191
r_nbtor_refined0.184
r_symmetry_vdw_other0.17
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.158
r_chiral_restr0.099
r_nbtor_other0.087
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2547
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing