6XDH

Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2

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	2020-04-24
Detector	RAYONIX MX-300
Wavelength(s)	0.9787
Spacegroup name	P 63
Unit cell lengths	150.820, 150.820, 112.570
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	45.210 - 2.350
R-factor	0.1581
Rwork	0.157
R-free	0.18250
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6vww
RMSD bond length	0.007
RMSD bond angle	0.801
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.18.2_3874)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.410
High resolution limit [Å]	2.350	10.510	2.350
Rmerge	0.077	0.039	0.594
Rmeas	0.081	0.041	0.621
Number of reflections	60593	707	4454
<I/σ(I)>	22.57	54.99	4.15
Completeness [%]	100.0	98.3	100
Redundancy	11.456	9.928	11.486
CC(1/2)	0.999	0.999	0.950

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	287	BewuA.18928.a.MX151.PW38806 at 36 mg/ml mixed 1:1 with Morpheus(G3): 10% (w/v) PEG 4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.02 M of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium l-tartrate, sodium oxamate. Tray: 315968g8, puck: teq6-3.