9OBA

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum containing phosphorylated active site histidine

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	69.665, 69.665, 315.755
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	47.930 - 1.580
R-factor	0.1451
Rwork	0.144
R-free	0.16810
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.049
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]	47.930	1.620
High resolution limit [Å]	1.580	1.580
Rmerge	0.122	0.836
Rmeas	0.125	0.911
Rpim	0.030	0.350
Total number of observations	1043431	28754
Number of reflections	63689	4551
<I/σ(I)>	15.7	1.8
Completeness [%]	99.9
Redundancy	16.4	6.3
CC(1/2)	0.998	0.721

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. Crystals were soaked with 10mM ATP for 4 hours which phosphorylated His139. No ADP bound after phosphorylation. plate Liu-S-177 D2, Puck: PSL-0411, Cryo: direct