9MGJ

Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (mannose bound)

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	2024-10-24
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	H 3 2
Unit cell lengths	93.012, 93.012, 130.529
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	46.510 - 1.180
R-factor	0.1284
Rwork	0.128
R-free	0.14670
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.952
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (dev_5438)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	68.550	1.210
High resolution limit [Å]	1.180	1.180
Rmerge	0.060	0.512
Rmeas	0.062	0.585
Rpim	0.014	0.272
Total number of observations	1087763	11671
Number of reflections	66110	2743
<I/σ(I)>	21.9	1.8
Completeness [%]	92.8
Redundancy	16.5	4.3
CC(1/2)	1.000	0.892

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.9	291	Morpheus F4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D-Glucosamine. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. mannose acquired from the crystallant. plate 14431 well H8 drop 3, Puck: PSL0916. Cryo: direct