9S27

Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose

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	2025-02-12
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.8731
Spacegroup name	H 3 2
Unit cell lengths	97.102, 97.102, 203.673
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	77.730 - 1.600
R-factor	0.1814
Rwork	0.181
R-free	0.19380
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.908
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]	77.730	1.630
High resolution limit [Å]	1.600	1.600
Rmerge	0.170	3.074
Rmeas	0.175	3.165
Rpim	0.041	0.750
Total number of observations	876921	41732
Number of reflections	48997	2380
<I/σ(I)>	14.5	1.3
Completeness [%]	100.0
Redundancy	17.9	17.5
CC(1/2)	0.999	0.295

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals of the SIRT3-[LTDi1-ADPR] complex (10.0 mg/mL SIRT3, 15 mM NAD+, 3 mM of LTDi1 with 1.5 % (v/v) final DMSO concentration) formed after 2 days in wells with an equal volume of 300 nL protein solution and 300 nL reservoir solution containing 3 M NaCl in 0.1 M Tris at pH 8.5.