13CV

Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide bound to Ubiquitin C-terminal Hydrolase-L3

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL12-2
Synchrotron site	SSRL
Beamline	BL12-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-12-13
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.98
Spacegroup name	P 1 21 1
Unit cell lengths	48.029, 85.605, 124.078
Unit cell angles	90.00, 96.81, 90.00

Refinement procedure

Resolution	42.800 - 1.940
R-factor	0.2047
Rwork	0.204
R-free	0.24370
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.015
RMSD bond angle	2.038
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHENIX
Refinement software	PHENIX ((1.20.1_4487: ???))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.020
High resolution limit [Å]	1.940	4.200	1.950
Rmerge	0.128	0.067	1.213
Rmeas	0.141	0.074	1.340
Rpim	0.058	0.031	0.560
Number of reflections	71476	7188	7025
<I/σ(I)>	8.2
Completeness [%]	98.2	96.5	97
Redundancy	5.5	5.5	5.3
CC(1/2)	0.995	0.996	0.592

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	298	200 mM Bis-Tris Propane 2.5 M Ammonium Sulfate