13RO

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004268

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL12-2
Synchrotron site	SSRL
Beamline	BL12-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-09-04
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.77488
Spacegroup name	P 43
Unit cell lengths	88.622, 88.622, 39.608
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	29.540 - 0.950
R-factor	0.1467
Rwork	0.146
R-free	0.16190
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]	44.310	44.310	0.970
High resolution limit [Å]	0.950	5.200	0.950
Rmerge	0.061	0.058	1.620
Rmeas	0.066	0.064	1.778
Rpim	0.025	0.026	0.718
Total number of observations	1299144	8184	52498
Number of reflections	191877	1250	8848
<I/σ(I)>	13.1	35	0.9
Completeness [%]	99.3	98.5	92.5
Redundancy	6.8	6.5	5.9
CC(1/2)	0.996	0.983	0.579

Crystallization Conditions

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