12XD

Room Temperature X-Ray Structure of SARS-CoV-2 Main Protease in Complex with noncovalent inhibitor KB-1

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	ROTATING ANODE
Source details	RIGAKU MICROMAX-007 HF
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-12-08
Detector	DECTRIS EIGER R 4M
Wavelength(s)	1.5406
Spacegroup name	I 1 2 1
Unit cell lengths	51.723, 81.575, 90.472
Unit cell angles	90.00, 96.65, 90.00

Refinement procedure

Resolution	29.440 - 2.000
R-factor	0.1803
Rwork	0.178
R-free	0.21800
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.522
Data reduction software	CrysalisPro
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	60.400	2.070
High resolution limit [Å]	2.000	2.000
Rmerge	0.061	0.200
Rpim	0.034	0.115
Number of reflections	25238	2522
<I/σ(I)>	26.37	6.21
Completeness [%]	99.9	99.7
Redundancy	4.5	3.9
CC(1/2)	0.975	0.958

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		287	18-21% PEG3350, and either 0.1 M Bis-Tris pH 6.5,7.0, or 0.1 M HEPES pH 7.0, 7.5