9PG6

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (NAD bound)

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	2025-04-25
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 1 21 1
Unit cell lengths	78.826, 130.061, 140.967
Unit cell angles	90.00, 90.86, 90.00

Refinement procedure

Resolution	49.030 - 2.150
R-factor	0.1947
Rwork	0.193
R-free	0.22970
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.763
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]	49.030	2.210
High resolution limit [Å]	2.150	2.150
Rmerge	0.184	1.251
Rmeas	0.199	1.346
Rpim	0.075	0.495
Total number of observations	1076571	82295
Number of reflections	153901	11373
<I/σ(I)>	7.8	1.6
Completeness [%]	99.8
Redundancy	7	7.2
CC(1/2)	0.996	0.742

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD added to the protein prior to crystallization. plate 19841 well A1 drop 2, Puck: PSL-2110, Cryo: 80% crystallant + 20% PEG 200