8ZLY

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and UDP

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL44XU
Synchrotron site	SPring-8
Beamline	BL44XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-12-04
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.900
Spacegroup name	P 21 21 2
Unit cell lengths	115.809, 403.204, 113.593
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.160 - 1.890
R-factor	0.16721
Rwork	0.165
R-free	0.20472
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.011
RMSD bond angle	1.719
Data reduction software	XDS
Data scaling software	XDS
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0238)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	48.170	48.170	2.000
High resolution limit [Å]	1.890	5.630	1.890
Rmerge	0.062	0.033	0.307
Rmeas	0.079	0.040	0.399
Number of reflections	423736	9892	51387
<I/σ(I)>	6.23
Completeness [%]	99.8
Redundancy	13.34
CC(1/2)	0.996	0.998	0.856

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.3	298	60 mM HEPES pH7.3, 75 mM NaCl, 75 mM KCl, 10 mM MgCl2, 75 mM Na formate, 14 % PEG3350, 10 mM oxalate, 10 mM FBP, 5 mM UDP