7ZS7
Crystal structure of human cathepsin L with covalently bound calpain inhibitor VI
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 | 2021-12-17 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 1.033 |
Spacegroup name | P 1 |
Unit cell lengths | 57.370, 62.560, 68.150 |
Unit cell angles | 105.48, 93.43, 115.52 |
Refinement procedure
Resolution | 44.400 - 1.600 |
R-factor | 0.1568 |
Rwork | 0.156 |
R-free | 0.18770 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3of9 |
RMSD bond length | 0.013 |
RMSD bond angle | 1.158 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHENIX (1.13-2998_9999) |
Refinement software | PHENIX (1.13-2998_9999) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.400 | 1.630 |
High resolution limit [Å] | 1.590 | 1.590 |
Rmeas | 0.323 | 1.677 |
Number of reflections | 101066 | 7218 |
<I/σ(I)> | 12.4 | |
Completeness [%] | 93.0 | 89.6 |
Redundancy | 18.4 | |
CC(1/2) | 0.997 | 0.840 |
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. |