8A4V

Crystal structure of human cathepsin L with covalently bound E-64

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	2021-10-04
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	1.033
Spacegroup name	P 1
Unit cell lengths	57.350, 62.750, 68.350
Unit cell angles	105.63, 93.32, 115.45

Refinement procedure

Resolution	44.420 - 1.650
R-factor	0.1621
Rwork	0.161
R-free	0.20290
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3of9
RMSD bond length	0.010
RMSD bond angle	0.890
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]	44.420	1.709
High resolution limit [Å]	1.650	1.650
Rmerge	0.311	2.574
Rmeas	0.336	2.774
Rpim	0.126	1.026
Number of reflections	95327	9473
<I/σ(I)>	5.97	1.15
Completeness [%]	97.6	96.99
Redundancy	7	7.2
CC(1/2)	0.989	0.368

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.