13DF

Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-methoxyphenyl)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	48.202, 85.305, 124.367
Unit cell angles	90.00, 97.63, 90.00

Refinement procedure

Resolution	42.680 - 1.840
R-factor	0.1965
Rwork	0.196
R-free	0.23790
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.096
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	1.920
High resolution limit [Å]	1.840	3.990	1.850
Rmerge	0.111	0.059	1.578
Rmeas	0.121	0.065	1.709
Rpim	0.047	0.026	0.650
Number of reflections	164183	8360	8400
<I/σ(I)>	7.9
Completeness [%]	97.9	95.6	98.7
Redundancy	6.4	6.2	6.6
CC(1/2)	0.991	0.995	0.491

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		298	Bis-Tris Propane Ammonium Sulfate