9S24

Crystal structure of human SIRT2 in complex with the covalent adduct of peptide triazole inhibitor OTDi1 and ADP-ribose

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID30B
Synchrotron site	ESRF
Beamline	ID30B
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-10-05
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.8731
Spacegroup name	P 43 21 2
Unit cell lengths	88.924, 88.924, 133.278
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	73.970 - 2.100
R-factor	0.2138
Rwork	0.213
R-free	0.22930
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.620
Data reduction software	autoPROC
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	88.920	2.160
High resolution limit [Å]	2.100	2.100
Rmerge	0.234	1.717
Rmeas	0.239	1.756
Rpim	0.048	0.365
Total number of observations	786456	58356
Number of reflections	31977	2585
<I/σ(I)>	12.7	2.6
Completeness [%]	100.0
Redundancy	24.6	22.6
CC(1/2)	0.998	0.310

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals of the SIRT2-[OTDi1-ADPR] complex (11.0 mg/mL SIRT2, 20 mM NAD+, 5 mM of OTDi1 with 2.5 % (v/v) final DMSO concentration) formed after one day in wells with an equal volume of protein solution and reservoir solution containing 26.5 % (w/v) PEG 3350 in 0.1 M HEPES at pH 7.5.