8F4Y

Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10

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	2021-06-09
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.12713
Spacegroup name	P 31 2 1
Unit cell lengths	171.040, 171.040, 52.029
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	29.620 - 2.130
R-factor	0.1584
Rwork	0.157
R-free	0.17980
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6w4h
RMSD bond length	0.004
RMSD bond angle	1.164
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	2.170
High resolution limit [Å]	2.130	2.130
Rmerge	0.104
Rmeas	0.113
Rpim	0.043	0.426
Number of reflections	49128	2485
<I/σ(I)>	17.5	2
Completeness [%]	99.9	100
Redundancy	6.9	7.1
CC(1/2)	0.993	0.718

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 3.83 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