13RK

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004052

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	2023-07-01
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.88557
Spacegroup name	P 43
Unit cell lengths	88.763, 88.763, 39.705
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	39.700 - 1.030
R-factor	0.1655
Rwork	0.164
R-free	0.18560
Structure solution method	MOLECULAR REPLACEMENT
Data reduction software	XDS (Jan 19, 2025 BUILT=20250430)
Data scaling software	Aimless (0.8.2)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	44.380	44.380	1.050
High resolution limit [Å]	1.030	5.640	1.030
Rmerge	0.051	0.025	2.819
Rmeas	0.056	0.027	3.079
Rpim	0.022	0.010	1.226
Total number of observations	991053	6866	46379
Number of reflections	152793	1006	7552
<I/σ(I)>	13.4	68.1	0.7
Completeness [%]	100.0	99.8	99.5
Redundancy	6.5	6.8	6.1
CC(1/2)	0.999	0.999	0.433

Crystallization Conditions

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