8TKZ

Structure of fission yeast Duf89 protein bound to Co2+ and PO4

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-06-16
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9795
Spacegroup name	P 21 21 21
Unit cell lengths	55.109, 91.163, 106.813
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	28.420 - 2.060
R-factor	0.1767
Rwork	0.174
R-free	0.22710
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.013
RMSD bond angle	1.180
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.100
High resolution limit [Å]	2.060	2.060
Rmerge	0.109	1.138
Rpim	0.039	0.425
Number of reflections	34041	1677
<I/σ(I)>	25.8	2
Completeness [%]	99.1	99.6
Redundancy	8
CC(1/2)	0.996	0.618

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		295	A solution containing 0.24 mM Duf89-D252N protein, 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18.2 mM Tris-HCl (pH 7.5), 136.2 mM NaCl, and 0.455 mM EDTA was preincubated on ice for 30 min. Aliquots were then mixed with equal volume of precipitant solution containing 0.01 M ZnSO4, 0.2 M MES (pH 6.5), and 25% (v/v) PEG-550 MME. Cryoprotectant: 100% paraffin oil