9JKL | pdb_00009jkl

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelITasser 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2960.1M Tris HCl pH 8.5, 8% W/V PEG 8000, 5mM Lysine
Crystal Properties
Matthews coefficientSolvent content
5.5677.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.015α = 90
b = 105.015β = 90
c = 241.35γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.379.221000.1380.1410.0280.99916.924.86097247.74
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.361001.5241.5560.3090.9592.625.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.379.226097230701000.2040.19110.2280.2148
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3927
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
DIALSdata collection
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction