6Z2E

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone

This is a non-PDB format compatible entry.

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	2020-04-22
Detector	DECTRIS PILATUS3 S 6M
Wavelength(s)	1.0332
Spacegroup name	P 61 2 2
Unit cell lengths	104.083, 104.083, 91.246
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	45.247 - 1.700
Rwork	0.192
R-free	0.24340
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6y2e
RMSD bond length	0.010
RMSD bond angle	1.814
Data reduction software	XDS
Data scaling software	SCALA (3.3.22)
Phasing software	MOLREP (11.7.02)
Refinement software	REFMAC (5.8.0257)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	45.620	1.790
High resolution limit [Å]	1.700	1.700
Rmerge	0.074	1.574
Rmeas	0.075	1.595
Rpim	0.012	0.257
Number of reflections	32640	4679
<I/σ(I)>	32.4
Completeness [%]	100.0	100
Redundancy	38.5	38
CC(1/2)	1.000	0.861

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	0.12 M Ethylene glycols (0.3 M Diethylene glycol, 0.3 M Triethylene glycol, 0.3 M Tetraethylene glycol, 0.3 M Pentaethylene glycol), 0.1 M buffer system 2 (1.0 M Sodium HEPES, MOPS (acid), pH 7.5), pH 7.5, 30% Precipitant mix 3 (20% glycerol, 10% PEG 4000)