8GM6

Structure of apurinic/apyrimidinic DNA lyase TK0353 from Thermococcus kodakarensis (Selenomethionine)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 23-ID-D
Synchrotron site	APS
Beamline	23-ID-D
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-03-22
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.9794
Spacegroup name	P 61 2 2
Unit cell lengths	99.542, 99.542, 159.507
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	43.100 - 1.980
R-factor	0.2021
Rwork	0.199
R-free	0.23330
Structure solution method	SAD
RMSD bond length	0.009
RMSD bond angle	0.995
Data reduction software	MOSFLM (7.4.0)
Data scaling software	Aimless (0.7.3)
Phasing software	CRANK2 (2.0.227)
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	43.100	2.020
High resolution limit [Å]	1.980	1.980
Rmerge	0.190	4.630
Rmeas	0.195	4.780
Rpim	0.046	1.180
Number of reflections	61936	3685
<I/σ(I)>	12.6	1.3
Completeness [%]	100.0	100
Redundancy	17.6	16.3
CC(1/2)	0.999	0.471

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8	297	2.5 M (NH4)2SO4 with 0.1 M Tris pH 8.0 mixed 1:1 with Protein at 20 mg/ml in 10 mM Tris pH 7.5, 100 mM NaCl, 10% glycerol and 1 mM DTT. Cryoprotection by addition of 1.5 M Li2SO4