7Z58

Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, DESY BEAMLINE P11
Synchrotron site	PETRA III, DESY
Beamline	P11
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-12-02
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	1.033
Spacegroup name	P 1
Unit cell lengths	57.180, 62.450, 67.820
Unit cell angles	105.58, 93.13, 115.56

Refinement procedure

Resolution	49.640 - 1.350
R-factor	0.1303
Rwork	0.130
R-free	0.15780
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7qkc
RMSD bond length	0.011
RMSD bond angle	1.086
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHENIX
Refinement software	PHENIX (1.18-3855_9999)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.640	1.398
High resolution limit [Å]	1.350	1.350
Rmerge	0.255	1.335
Rmeas	0.257	1.364
Rpim	0.031	0.277
Number of reflections	175672	17547
<I/σ(I)>	16.83	2.11
Completeness [%]	100.0	99.9
Redundancy	61.1	23.1
CC(1/2)	0.999	0.835

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4	293	Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew at 293 K to final size after approximately 3 days, were transferred to a compound soaking solution containing 22% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0 as well as 5% v/v DMSO and 10% v/v PEG 400.