7Z1X

Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Synchrotron site	PETRA III, EMBL c/o DESY
Beamline	P13 (MX1)
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-08-15
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.976255
Spacegroup name	P 31
Unit cell lengths	108.353, 108.353, 124.041
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	93.840 - 1.860
R-factor	0.2238
Rwork	0.212
R-free	0.24940
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6n9o 5ivo
RMSD bond length	0.008
RMSD bond angle	0.774
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX ((1.20_4444: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	93.840	1.926
High resolution limit [Å]	1.860	1.860
Rmerge	0.016	0.855
Rmeas	0.023
Rpim	0.016	0.855
Number of reflections	136585	13351
<I/σ(I)>	17.43	0.73
Completeness [%]	99.7
Redundancy	2
CC(1/2)	1.000	0.443

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4.4	293	20 mg/ml protein complex; 0.04 M NaCl, 25.8% (v/v) PEG400, 0.05 M Na3Cit pH 4.4