8A4Y

SARS-CoV-2 non-structural protein-1 (nsp1) in complex with N-(2,3-dihydro-1H-inden-5-yl)acetamide

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE MASSIF-1
Synchrotron site	ESRF
Beamline	MASSIF-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-08
Detector	DECTRIS PILATUS3 2M
Wavelength(s)	0.96546
Spacegroup name	P 43 21 2
Unit cell lengths	36.688, 36.688, 140.928
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	35.505 - 1.099
R-factor	0.1477
Rwork	0.147
R-free	0.16640
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7k7p
RMSD bond length	0.012
RMSD bond angle	1.270
Data reduction software	autoPROC (v1.0)
Data scaling software	autoPROC (v1.0)
Phasing software	PHENIX (1.19_4092)
Refinement software	PHENIX (1.19_4092)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	35.505	1.120
High resolution limit [Å]	1.099	1.100
Rmeas	0.067	0.750
Rpim	0.020	0.291
Number of reflections	40443	1953
<I/σ(I)>	18.4	2.3
Completeness [%]	99.9	98.1
Redundancy	11.5	6.3
CC(1/2)	0.998	0.801

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		291.15	Commercial screen Index 44 (0.1 M HEPES pH 7.5, 25% w/v PEG3350) was chosen for SARS-CoV-2 nsp1 (residues 10 to 126) crystallisation in large quantities using hanging drop method. Frozen stocks of SARS-CoV-2 nsp1 (residues 10 to 126) were thawed on ice and centrifuged in a Thermo Scientific Pico 17 Microcentrifuge, 24-Pl Rotor at 4 degrees, 20000 rpm for 10 min to remove aggregates before the determination of the protein concentration. Subsequently, the protein stock was diluted to 20 mg/mL with precrystallisation buffer (10 mM HEPES and 300 mM NaCl). 400 uL of Index condition 44 was added into each reservoir well. Five protein drops were set on each cover slip by mixing 1 uL of protein solution with 1 uL of the reservoir. The 24-well Linbro plates were incubated at 18 degrees.