13RM

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004100

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL9-2
Synchrotron site	SSRL
Beamline	BL9-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-08-11
Detector	Dectris Pilatus 6M PAD
Wavelength(s)	0.88557
Spacegroup name	P 43
Unit cell lengths	88.830, 88.830, 39.420
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	39.730 - 1.010
R-factor	0.1362
Rwork	0.136
R-free	0.14930
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]	44.420	44.420	1.030
High resolution limit [Å]	1.010	5.530	1.010
Rmerge	0.040	0.025	0.770
Rmeas	0.044	0.027	0.840
Rpim	0.017	0.010	0.332
Total number of observations	1047451	7505	48237
Number of reflections	159544	1066	7747
<I/σ(I)>	21.5	79.7	2.2
Completeness [%]	99.1	99.7	98.1
Redundancy	6.6	7	6.2
CC(1/2)	1.000	0.999	0.831

Crystallization Conditions

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