6WRT

Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) C70A/S158C 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 to 8.2
Crystal Properties
Matthews coefficientSolvent content
2.5752.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.78α = 90
b = 101.78β = 90
c = 71.56γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.00ALS5.0.2

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
11.5545.5299.90.99913.1213.455943
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)
11.551.651000.4150.9613.1

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-VALUE4NDA1.5545.521.3554871140099.80.18210.18130.214634.63
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_d23.792
f_angle_d1.3304
f_chiral_restr0.0946
f_bond_d0.0161
f_plane_restr0.0101
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2479
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms33

Software

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