Experiment: 6L3Y

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-C

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PG3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.09M NPS-0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic,0.3M Ammonium sulfate. 1.0M Buffer-pH6.5- Imidazole; MES monohydrate (acid) Precipitant Mix-25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 299.841	α = 90
b = 52.831	β = 90
c = 70.44	γ = 90

Symmetry
Space Group	P 21 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	293	PIXEL	DECTRIS EIGER X 16M		2019-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.89	149.921	100	0.989	5.7	13.3		25891

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.898	2.948	100		0.446	0.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4PG3	3.1	74.96	1.34	21199	1059	99.81	0.228	0.2252	0.2252	0.2799	0.2773	57.6733

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	7899
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	89

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing