13RS

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005707

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	2024-12-13
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.77488
Spacegroup name	P 43
Unit cell lengths	88.891, 88.891, 39.528
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	29.630 - 0.940
R-factor	0.1447
Rwork	0.144
R-free	0.15910
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]	39.750	39.750	0.960
High resolution limit [Å]	0.940	5.150	0.940
Rmerge	0.036	0.019	1.591
Rmeas	0.040	0.021	1.785
Rpim	0.015	0.008	0.791
Total number of observations	1322471	8957	45040
Number of reflections	199729	1321	9380
<I/σ(I)>	19	66.9	0.8
Completeness [%]	99.7	99.5	95.2
Redundancy	6.6	6.8	4.8
CC(1/2)	0.999	0.995	0.381

Crystallization Conditions

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