8DF8

Structure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA complex

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2020-11-04
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 43 21 2
Unit cell lengths	120.941, 120.941, 497.569
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	58.760 - 2.920
R-factor	0.2587
Rwork	0.257
R-free	0.28770
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	8df7
RMSD bond length	0.002
RMSD bond angle	0.489
Data reduction software	XDS
Data scaling software	STARANISO
Phasing software	PHASER
Refinement software	BUSTER

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	108.800	3.240
High resolution limit [Å]	2.920	2.920
Rmerge	0.081	1.605
Rmeas	0.084	1.650
Number of reflections	56136	51701
<I/σ(I)>	21	1.7
Completeness [%]	69.0	12.9
Redundancy	13.9	18.7
CC(1/2)	1.000	0.744

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	5.5	303	Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. Crystals started to appear within minutes of setting up the trays in 1:1 or 2:1 well to complex ratio. Well solution: 2 ul:1 ul (reaction:well solution), 2% PEG 8K, 24 mM sodium acetate pH 5.1, 26 mM sodium acetate pH 5.6, 12.5 uM phosphotungstic acid. 5X DNA binding buffer: 250 mM sodium acetate pH 5.0 at 65C, 150 mM sodium chloride, 5 mM magnesium chloride.