39AC

Crystal structure of a Nucleoside diphosphate kinase from Treponema pallidum (ADP complex)

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	2026-08-01
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 1
Unit cell lengths	115.785, 115.857, 128.600
Unit cell angles	90.08, 106.37, 119.90

Refinement procedure

Resolution	48.830 - 2.490
R-factor	0.2179
Rwork	0.209
R-free	0.25650
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.766
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5936: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.830	2.550
High resolution limit [Å]	2.490	2.490
Rmerge	0.177	0.853
Rmeas	0.209	1.009
Rpim	0.110	0.531
Total number of observations	665893	49098
Number of reflections	186433	13860
<I/σ(I)>	6.3	1.5
Completeness [%]	97.2
Redundancy	3.6	3.5
CC(1/2)	0.984	0.499

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	Morpheus A10: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2, TrpaC.01302.a.B1.PW39573 at 25.4 mg/mL. Cocrystallization with ATP and crystals soaked with extra ATP but only ADP was bound based on the electron density. plate 21256 A10 d2, Puck: PSL-1603, Cryo: direct. Crystal was consistent with C2 space group. However, MR gave a strange solution with a) clashes; b) some open hexamers; c) biased density from over averaging related to b); and order-disorder layers in the density. The best result was obtained using with pseudo-merohedral twinning in P1 (-h-k,k,-l)