13VC

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000681

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	2023-03-09
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.88557
Spacegroup name	P 43
Unit cell lengths	88.785, 88.785, 39.527
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.390 - 1.000
R-factor	0.1596
Rwork	0.159
R-free	0.17300
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]	44.390	44.390	1.020
High resolution limit [Å]	1.000	5.480	1.000
Rmerge	0.050	0.025	1.781
Rmeas	0.055	0.027	2.037
Rpim	0.022	0.010	0.957
Total number of observations	1049995	7580	34160
Number of reflections	166158	1095	8171
<I/σ(I)>	13	55.6	0.6
Completeness [%]	99.9	99.8	99
Redundancy	6.3	6.9	4.2
CC(1/2)	0.999	1.000	0.348

Crystallization Conditions

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