9AZX

Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with NDPr

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	CHESS BEAMLINE 7B2
Synchrotron site	CHESS
Beamline	7B2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-01-26
Detector	DECTRIS EIGER2 S 16M
Wavelength(s)	0.96860
Spacegroup name	P 1
Unit cell lengths	45.496, 47.084, 65.726
Unit cell angles	79.15, 72.05, 74.30

Refinement procedure

Resolution	29.060 - 1.395
R-factor	0.153
Rwork	0.152
R-free	0.18440
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6ywl
RMSD bond length	0.010
RMSD bond angle	1.093
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21_5207)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	29.060	1.430
High resolution limit [Å]	1.395	1.395
Rmerge	0.054	0.601
Rmeas	0.064	0.747
Rpim	0.034	0.434
Number of reflections	93149	5586
<I/σ(I)>	12.18	1.38
Completeness [%]	94.3	78.78
Redundancy	3.5	2.7
CC(1/2)	0.998	0.728

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM Tris-HCl, pH 8, 200 mM sodium acetate, 30% w/v PEG4000