9OAI

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with thymidine-5'-phosphate

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	69.879, 69.879, 316.209
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	48.050 - 1.510
R-factor	0.1432
Rwork	0.142
R-free	0.16300
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	1.030
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]	48.050	1.550
High resolution limit [Å]	1.510	1.510
Rmerge	0.093	0.737
Rmeas	0.096	0.824
Rpim	0.023	0.356
Total number of observations	1085637	19240
Number of reflections	70384	3961
<I/σ(I)>	20	1.7
Completeness [%]	96.3
Redundancy	15.4	4.9
CC(1/2)	0.999	0.669

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. plate Liu-S-177 D2, Puck: PSL-0505, Cryo: direct from soaking solution