9OB9

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with ADP and CTP

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	69.784, 69.784, 315.704
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	47.980 - 1.600
R-factor	0.1515
Rwork	0.150
R-free	0.17850
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	1.161
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]	47.980	1.640
High resolution limit [Å]	1.600	1.600
Rmerge	0.102	0.920
Rmeas	0.105	0.991
Rpim	0.025	0.361
Total number of observations	1030537	31376
Number of reflections	61450	4320
<I/σ(I)>	18.9	1.7
Completeness [%]	99.7
Redundancy	16.8	7.3
CC(1/2)	0.999	0.816

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 ADP and CTP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Partial ADP and CTP occupancy at same sites. plate Liu-S-177 D2, Puck: PSL-0514, Cryo: direct from soaking solution