9Y4U

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)

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	2025-08-09
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	I 2 2 2
Unit cell lengths	87.189, 123.985, 130.745
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.190 - 1.900
R-factor	0.1769
Rwork	0.175
R-free	0.21440
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.131
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5778: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.190	1.940
High resolution limit [Å]	1.900	1.900
Rmerge	0.069	1.743
Rmeas	0.072	1.813
Rpim	0.020	0.495
Total number of observations	744592	47577
Number of reflections	56062	3590
<I/σ(I)>	18.9	1.5
Completeness [%]	100.0
Redundancy	13.3	13.3
CC(1/2)	1.000	0.748

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	Berkeley D4: 25% (w/v) PEG 3350, 100 mM sodium acetate pH 4.5. 2mM NAD addied prior to crystallization, plate 20205 well D4 drop 3 , Puck: PSL2003, Cryo: 80% crystallant + 20% PEG 200