9S3J

Crystal structure of the human tumor necrosis factor receptor 1 extracellular domain in complex with a picolinic acid based ligand at 1.77A resolution

This is a non-PDB format compatible entry.

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	68.629, 68.629, 186.101
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	25.230 - 1.770
R-factor	0.2286
Rwork	0.227
R-free	0.25150
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.013
RMSD bond angle	1.244
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]	48.530	1.830
High resolution limit [Å]	1.770	1.770
Rmerge	0.146	4.551
Rmeas	0.149	4.641
Rpim	0.029	0.900
Total number of observations	1171902	110895
Number of reflections	44442	4267
<I/σ(I)>	15.1	0.9
Completeness [%]	100.0
Redundancy	26.4	26
CC(1/2)	0.999	0.071

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) Mixed in 3.5:1 (protein/reservoir)