7NXM

Structure of human cathepsin K in complex with the selective activity-based probe Gu3416

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	ROTATING ANODE
Source details	RIGAKU MICROMAX-007
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-03-05
Detector	DECTRIS PILATUS 300K
Wavelength(s)	1.541870
Spacegroup name	P 2 21 21
Unit cell lengths	32.045, 71.677, 80.856
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	35.860 - 1.720
Rwork	0.160
R-free	0.17840
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5tdi
RMSD bond length	0.012
RMSD bond angle	1.633
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0267)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	1.840	1.750
High resolution limit [Å]	1.720	1.800	1.720
Rmerge	0.061	0.286	0.423
Rmeas	0.079	0.397	0.598
Rpim	0.050	0.274	0.423
Number of reflections	17548	772	153
<I/σ(I)>	27.18	3.1	1.4
Completeness [%]	85.7	74.9	14.8
Redundancy	3.8	2.8	1.3
CC(1/2)	0.996	0.881	0.678

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5. Morpheus C4 condition