9D6H

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-1504

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ALS BEAMLINE 8.3.1
Synchrotron site	ALS
Beamline	8.3.1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-05-20
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.88557
Spacegroup name	P 43
Unit cell lengths	88.882, 88.882, 39.587
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.440 - 1.020
R-factor	0.1347
Rwork	0.134
R-free	0.14960
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.870
Data reduction software	XDS (Jun 30, 2023)
Data scaling software	XDS (Jun 30, 2023)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21.1_5286)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	44.440	1.040
High resolution limit [Å]	1.020	1.020
Rmerge	0.051	0.906
Rmeas	0.056	1.004
Rpim	0.022	0.421
Total number of observations	994507	39722
Number of reflections	156619	7343
<I/σ(I)>	15.4	1.2
Completeness [%]	99.7
Redundancy	6.3	5.4
CC(1/2)	0.999	0.678

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	9.5	292	100 mM CHES, 28% PEG 3000