9OAK

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate

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	2025-04-05
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 65 2 2
Unit cell lengths	69.734, 69.734, 316.121
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	47.990 - 1.610
R-factor	0.1462
Rwork	0.145
R-free	0.17150
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.047
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5669: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.990	1.650
High resolution limit [Å]	1.610	1.610
Rmerge	0.099	0.869
Rmeas	0.102	0.934
Rpim	0.024	0.335
Total number of observations	1023118	32252
Number of reflections	60534	4362
<I/σ(I)>	19.8	1.8
Completeness [%]	100.0
Redundancy	16.9	7.4
CC(1/2)	0.999	0.765

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Subunit A contains partially occupied CTP and HIP from reaction. Subunit C contains partially occupied CDP and HIP. plate Liu-S-177 D2, Puck: PSL-0503, Cryo: direct from soaking solution