9F3V

RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor

This is a non-PDB format compatible entry.

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	2023-06-20
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.9655
Spacegroup name	P 21 21 21
Unit cell lengths	54.824, 90.750, 137.976
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	54.981 - 1.943
Rwork	0.220
R-free	0.25640
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	1.084
Data reduction software	autoPROC
Data scaling software	autoPROC
Refinement software	REFMAC (5.8.0419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	54.981	1.976
High resolution limit [Å]	1.943	1.943
Rmerge	0.093	2.848
Rmeas	0.104	3.171
Number of reflections	48396	2449
<I/σ(I)>	8	0.4
Completeness [%]	96.1	95.5
Redundancy	5.3
CC(1/2)	0.996	0.393

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Compound 37, in powder form was solubilized in DMSO at 5 mM concentration. One aliquot of protein at 1.14 mg/ml was thawed and mixed with 50 microM inhibitor and kept on ice for 10 minutes. The complex was than concentrated to 3.8 mg/ml. solutions containing 3.8 mg/ml of protein-inhibitor complex equilibrated against 0.1 M citric acid and 0.8 M sodium formate at pH 5.