6WRN

Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) C70A variant bound to 3-nitro-tyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NDA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29822-23% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris pH 7.9-8.2
Crystal Properties
Matthews coefficientSolvent content
2.5952.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.19α = 90
b = 102.19β = 90
c = 71.48γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152018-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.641.5799.80.99912.993050272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.799.50.4920.9830.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4NDA1.641.571.3650245199799.690.18670.18550.215235.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d24.4314
f_angle_d1.4269
f_chiral_restr0.098
f_bond_d0.0174
f_plane_restr0.0087
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2504
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms17

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
XSCALEdata scaling
XDSdata processing
XDSdata reduction