9GEF

Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex

Experimental procedure

Experimental method	MAD
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I23
Synchrotron site	Diamond
Beamline	I23
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-09-23
Detector	DECTRIS PILATUS 12M
Wavelength(s)	2.75, 3.14, 3.54, 4.35, 4.50 and 5.16
Spacegroup name	P 31 2 1
Unit cell lengths	158.533, 158.533, 210.820
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	79.390 - 2.620
R-factor	0.18089
Rwork	0.180
R-free	0.20850
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.013
RMSD bond angle	1.440
Data reduction software	DIALS
Data scaling software	xia2.multiplex
Phasing software	DIMPLE
Refinement software	PDB-REDO (8.11)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	210.820	2.410
High resolution limit [Å]	2.370	2.370
Rmerge	0.215	5.369
Rpim	0.027	0.796
Number of reflections	124385	6112
<I/σ(I)>	11.6
Completeness [%]	100.0	100
Redundancy	59.4	45
CC(1/2)	0.999	0.204

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were cryoprotected with 50 mM sodium cacodylate pH 6.5, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 1 mM beta-mercaptoethanol and 30% v/v MPD before being flash-cooled in liquid nitrogen and collected in elliptical polyimide sample mounts.