9U7D

Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL19U1
Synchrotron site	SSRF
Beamline	BL19U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-01-12
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97861
Spacegroup name	I 41 2 2
Unit cell lengths	111.639, 111.639, 220.006
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	64.140 - 2.700
R-factor	0.2044
Rwork	0.203
R-free	0.23130
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.208
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	PHENIX ((1.18.2_3874: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	99.560	2.830
High resolution limit [Å]	2.700	2.700
Rmerge	0.511	1.902
Rmeas	0.521	1.941
Rpim	0.103	0.386
Number of reflections	18747	2549
<I/σ(I)>	10.1	1.9
Completeness [%]	95.9	100
Redundancy	24.9
CC(1/2)	0.993	0.432

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	6% (w/v) PEG8000, 100 mM MES/Sodium hydroxide pH 6.0, 200 mM zinc acetate and 20% PEG400