9SFB | pdb_00009sfb

Structure at 2.7 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to a tRNA(Tyr)(GUA) transcript, the sulphamoyl analogue of tyrosyl-adenylate and pyrophosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H3F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP288Don't know
Crystal Properties
Matthews coefficientSolvent content
3.5164.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.629α = 90
b = 130.629β = 90
c = 109.086γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
12.72397.060.06386.229086
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)
12.72.7797.80.352

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.72329086144997.0570.2060.20420.21120.24790.253988.246
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]
1.4590.731.459-4.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.668
r_dihedral_angle_6_deg13.167
r_lrange_it10.292
r_lrange_other10.291
r_scangle_it7.725
r_scangle_other7.724
r_mcangle_it5.774
r_mcangle_other5.774
r_dihedral_angle_1_deg5.609
r_dihedral_angle_2_deg5.484
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.668
r_dihedral_angle_6_deg13.167
r_lrange_it10.292
r_lrange_other10.291
r_scangle_it7.725
r_scangle_other7.724
r_mcangle_it5.774
r_mcangle_other5.774
r_dihedral_angle_1_deg5.609
r_dihedral_angle_2_deg5.484
r_scbond_it4.907
r_scbond_other4.906
r_mcbond_it3.802
r_mcbond_other3.796
r_angle_refined_deg1.072
r_angle_other_deg0.381
r_dihedral_angle_other_2_deg0.283
r_nbtor_refined0.196
r_nbd_refined0.191
r_symmetry_nbd_other0.187
r_symmetry_xyhbond_nbd_refined0.153
r_nbd_other0.132
r_xyhbond_nbd_refined0.129
r_symmetry_nbd_refined0.125
r_symmetry_nbtor_other0.074
r_chiral_restr0.046
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_symmetry_xyhbond_nbd_other0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3393
Nucleic Acid Atoms1753
Solvent Atoms
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing