8F4S

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-D
Synchrotron site	APS
Beamline	21-ID-D
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-03-02
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.12705
Spacegroup name	P 31 2 1
Unit cell lengths	170.847, 170.847, 51.881
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	29.590 - 2.150
R-factor	0.1669
Rwork	0.166
R-free	0.19090
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6w4h
RMSD bond length	0.004
RMSD bond angle	1.214
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHASER
Refinement software	REFMAC (5.8.0350)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	30.000	2.190
High resolution limit [Å]	2.150	2.150
Rmerge	0.178
Rmeas	0.183
Rpim	0.040	0.756
Number of reflections	47404	2327
<I/σ(I)>	24.4	1.7
Completeness [%]	99.9	100
Redundancy	20.6	21.2
CC(1/2)	0.996	0.575

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 4 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 5% Glycerol; Screen: Anions (B2), 0.1M HEPES pH 7.5, 1.25M Sodium acetate; Soaks: Compound 5a, 24 hours; Cryo: 4M Sodium formate