2DLC

Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Tris, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.854α = 90
b = 63.854β = 90
c = 330.334γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4rMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.9798, 0.9801, 0.9819, 0.9727SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.44099.40.04811.74.127897
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5399.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.44026411140399.30.247070.244910.28889RANDOM32.966
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.3
r_angle_refined_deg1.124
r_scangle_it0.742
r_scbond_it0.521
r_mcangle_it0.477
r_mcbond_it0.253
r_nbd_refined0.176
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.3
r_angle_refined_deg1.124
r_scangle_it0.742
r_scbond_it0.521
r_mcangle_it0.477
r_mcbond_it0.253
r_nbd_refined0.176
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.071
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2698
Nucleic Acid Atoms1472
Solvent Atoms57
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SHARPphasing