9HH5

Crystal Structure of nsp15 Endoribonuclease from SARS CoV-2 in Complex with Sepantronium (YM-155)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, DESY BEAMLINE P11
Synchrotron site	PETRA III, DESY
Beamline	P11
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-12-14
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.033
Spacegroup name	P 63
Unit cell lengths	151.408, 151.408, 109.302
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	45.140 - 2.080
R-factor	0.19198
Rwork	0.191
R-free	0.20526
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.708
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	REFMAC (5.8.0430)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	45.140	2.120
High resolution limit [Å]	2.080	2.080
Rmerge	0.064	1.396
Rmeas	0.077
Rpim		0.936
Number of reflections	85181	4535
<I/σ(I)>	12.6
Completeness [%]	99.7	99.9
Redundancy	5.8
CC(1/2)	0.999	0.502

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	0.1 M Tris pH 8.5, 10 % w/v Peg 4000, 0.15 mM sodium acetate