9YON

Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-06-07
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 31 2 1
Unit cell lengths	106.660, 106.660, 185.480
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	46.230 - 2.430
R-factor	0.2028
Rwork	0.201
R-free	0.23320
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.544
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5723: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.370	2.654
High resolution limit [Å]	2.430	2.434
Rmerge	0.112	2.254
Rmeas	0.115	2.311
Rpim	0.026	0.510
Total number of observations		35561
Number of reflections	35030	1751
<I/σ(I)>	17.3	1.6
Completeness [%]	75.3
Redundancy	19.2	20.3

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5	291	Grid Salt screen H8 : 4.0M NaCl, 0.1M Citric acid/citrate, pH 5.0. CrpaA.01302.a.B2.PW39348 at 21.9 mg/mL. 2mM inhibitor added to the protein prior to crystallization. plate 19968 H8 drop 1, Puck: PSL-1107, Cryo: 2.5M Lithium sulfate. The data were somewhat anisotropic which produced residual density (Fo-Fc) thoughout the polypeptide. The anisotropically truncated data from staraniso were used for refinement. The original and anisotropic truncated data were both deposited.