9OAN

Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with guanosine-5'-diphosphate and AMP-PNP

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	69.829, 69.829, 316.142
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	48.030 - 1.630
R-factor	0.1508
Rwork	0.150
R-free	0.17080
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.117
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]	48.030	1.670
High resolution limit [Å]	1.630	1.630
Rmerge	0.106	0.993
Rmeas	0.109	1.055
Rpim	0.025	0.346
Total number of observations	1010359	34813
Number of reflections	58143	3978
<I/σ(I)>	18.7	1.7
Completeness [%]	99.4
Redundancy	17.4	8.8
CC(1/2)	0.999	0.718

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 ANP and GDP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Ligands only bound if ANP is present. GDP only soaks did not produce binding. plate Liu-S-177 D2, Puck: PSL-0509, Cryo: direct from soaking solution