9S3I

Crystal structure of the human tumor necrosis factor receptor 1 extracellular domain at 1.64A resolution

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	MAX IV BEAMLINE BioMAX
Synchrotron site	MAX IV
Beamline	BioMAX
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-10-06
Detector	DECTRIS EIGER2 XE CdTe 16M
Wavelength(s)	0.7293
Spacegroup name	P 41 21 2
Unit cell lengths	69.221, 69.221, 185.186
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	27.720 - 1.640
R-factor	0.2068
Rwork	0.205
R-free	0.23790
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.129
Data reduction software	XDS (v1.20)
Data scaling software	Aimless (v0.8.1)
Phasing software	PHASER (v2.8.3)
Refinement software	PHENIX (v1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.950	1.700
High resolution limit [Å]	1.640	1.640
Rmerge	0.112	5.972
Rmeas	0.114	6.158
Rpim	0.023	1.480
Total number of observations	1405593	90628
Number of reflections	56257	5413
<I/σ(I)>	16.5	0.5
Completeness [%]	100.0
Redundancy	25	16.7
CC(1/2)	0.999	0.117

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Crystallization cocktail: 0.1 M HEPES, 70% v/v 2-Methyl-2,4-pentanediol (pH 7.5) Additive cocktail: 0.2% w/v 1,4-diaminobutane, 0.2% w/v 1,8-diaminooctane, 0.2% w/v cadaverine, 0.2% w/v cystamine dihydrochloride, 0.2% w/v Spermidine, 0.02 M HEPES sodium (pH 6.8) Mixed in 3.5:1:1 (protein/reservoir/additives)