9ZAO

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)

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	2025-06-28
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 1
Unit cell lengths	76.358, 139.715, 222.702
Unit cell angles	76.30, 87.32, 88.12

Refinement procedure

Resolution	48.290 - 3.090
R-factor	0.1834
Rwork	0.181
R-free	0.23350
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.766
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]	48.290	3.170
High resolution limit [Å]	3.090	3.090
Rmerge	0.102	1.004
Rmeas	0.121	1.175
Rpim	0.064	0.606
Total number of observations	563752	44015
Number of reflections	159633	11904
<I/σ(I)>	10	1.4
Completeness [%]	97.5
Redundancy	3.5	3.7
CC(1/2)	0.995	0.689

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct