13RP

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004272

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	88.674, 88.674, 39.519
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	28.040 - 0.950
R-factor	0.1414
Rwork	0.141
R-free	0.15530
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]	44.340	44.340	0.970
High resolution limit [Å]	0.950	5.200	0.950
Rmerge	0.068	0.062	1.314
Rmeas	0.074	0.067	1.443
Rpim	0.028	0.026	0.584
Total number of observations	1293708	8401	51971
Number of reflections	191837	1255	8929
<I/σ(I)>	12	30.4	0.9
Completeness [%]	99.3	98.6	93.2
Redundancy	6.7	6.7	5.8
CC(1/2)	0.998	0.992	0.532

Crystallization Conditions

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