9S23

Crystal structure of human SIRT2 in complex with peptide triazole inhibitor OTDi1

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID23-2
Synchrotron site	ESRF
Beamline	ID23-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-11-06
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.8731
Spacegroup name	P 43 21 2
Unit cell lengths	89.621, 89.621, 133.033
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	53.410 - 2.300
R-factor	0.2278
Rwork	0.226
R-free	0.25900
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.541
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]	74.330	2.380
High resolution limit [Å]	2.300	2.300
Rmerge	0.352	3.592
Rmeas	0.358	3.659
Rpim	0.069	0.693
Total number of observations	658807	64498
Number of reflections	24808	2368
<I/σ(I)>	12.5	1.3
Completeness [%]	100.0
Redundancy	26.6	27.2
CC(1/2)	0.998	0.335

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals of the SIRT2-OTDi1 complex (11.0 mg/mL SIRT2, 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 21.5 % (w/v) PEG 3350 in 0.1 M Bis-Tris at pH 6.7.