Experiment: 9JKL

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ITasser

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		296	0.1M Tris HCl pH 8.5, 8% W/V PEG 8000, 5mM Lysine

Crystal Properties
Matthews coefficient	Solvent content
5.56	77.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.015	α = 90
b = 105.015	β = 90
c = 241.35	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2022-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	79.22	100	0.138	0.141	0.028	0.999	16.9	24.8		60972			47.74

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)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	100		1.524	1.556	0.309	0.959	2.6	25.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	79.22	60972	3070	100	0.204	0.1911	0.228	0.2148

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 Atoms	Number
Protein Atoms	3927
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
DIALS	data collection
Aimless	data scaling
PHASER	phasing
MOSFLM	data reduction