8YBL

Crystal structure of nanobody SEB-Nb3 bound to staphylococcal enterotoxin B (SEB)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL10U2
Synchrotron site	SSRF
Beamline	BL10U2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-12-16
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.979183
Spacegroup name	P 21 21 21
Unit cell lengths	57.570, 83.751, 86.972
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	60.330 - 2.330
R-factor	0.22506
Rwork	0.223
R-free	0.26163
Structure solution method	MOLECULAR REPLACEMENT
Data reduction software	XDS
Data scaling software	Aimless (0.7.7)
Phasing software	PHASER (2.8.3)
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	60.330	2.450
High resolution limit [Å]	2.330	2.330
Rmerge	0.284	1.378
Rmeas	0.310	1.518
Rpim	0.123	0.627
Total number of observations	115931	15453
Number of reflections	18666	2664
<I/σ(I)>	5.4	1.5
Completeness [%]	100.0
Redundancy	6.2	5.8
CC(1/2)	0.982	0.460

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION		298	8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350