13RW

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006354

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	2024-10-16
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.88557
Spacegroup name	P 43
Unit cell lengths	88.754, 88.754, 39.576
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	39.690 - 1.080
R-factor	0.1592
Rwork	0.158
R-free	0.18170
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	1.100
High resolution limit [Å]	1.080	5.920	1.080
Rmerge	0.071	0.023	2.645
Rmeas	0.077	0.025	2.885
Rpim	0.030	0.010	1.140
Total number of observations	856959	5958	39774
Number of reflections	132096	874	6408
<I/σ(I)>	12	67.4	0.7
Completeness [%]	99.9	99.8	98.5
Redundancy	6.5	6.8	6.2
CC(1/2)	0.999	0.999	0.410

Crystallization Conditions

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