8XW8

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

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	2023-10-12
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.900
Spacegroup name	C 1 2 1
Unit cell lengths	123.335, 256.080, 88.575
Unit cell angles	90.00, 90.04, 90.00

Refinement procedure

Resolution	47.300 - 2.000
R-factor	0.19985
Rwork	0.198
R-free	0.23364
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.019
RMSD bond angle	1.832
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]	47.300	47.300	2.120
High resolution limit [Å]	2.000	5.950	2.000
Rmerge	0.112	0.037	0.912
Rmeas	0.120	0.040	0.985
Number of reflections	181214	6961	28831
<I/σ(I)>	16.79
Completeness [%]	97.9
Redundancy	7.2
CC(1/2)	0.998	0.999	0.821

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8	298	10mM HEPES pH7.5, 250mM NaCl, 75mM KCl, 20% PEG1000, 5% glycerol, 50mM tricine pH8.0, 10mM Oxalate, 10mM FBP, 5mM GDP