9PFY

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with ATP

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	2025-05-25
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 65 2 2
Unit cell lengths	69.815, 69.815, 315.861
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	48.010 - 1.420
R-factor	0.1284
Rwork	0.127
R-free	0.15580
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	1.015
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]	48.010	1.460
High resolution limit [Å]	1.420	1.420
Rmerge	0.071	0.618
Rmeas	0.073	0.700
Rpim	0.017	0.318
Total number of observations	1338263	26438
Number of reflections	86973	5944
<I/σ(I)>	23.3	1.8
Completeness [%]	99.5
Redundancy	15.4	4.4
CC(1/2)	1.000	0.720

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	Berkeley F12: 35% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystal was transferred to 35% MPD, 100mM Bis-Tris, pH 5.5, 100mM sodium formate two times and then soaked with in the same solution containing 10mM ATP for 3 hours. Subunits A and C have partial occupancy of ATP and HIP in the active site. Subunit B had 100% conversion to HIP. plate Liu-S-177 D2, Puck: PSL-0105, Cryo: direct from soaking solution