7QKB
Crystal structure of human Cathepsin L in complex with covalently bound GC376
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 | 2021-08-07 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 1.033 |
Spacegroup name | P 1 |
Unit cell lengths | 57.290, 62.450, 67.820 |
Unit cell angles | 105.31, 93.52, 115.93 |
Refinement procedure
Resolution | 44.250 - 1.800 |
R-factor | 0.1701 |
Rwork | 0.169 |
R-free | 0.20300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3of9 |
RMSD bond length | 0.006 |
RMSD bond angle | 0.652 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX |
Refinement software | PHENIX (1.18-3855_9999) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.250 | 1.864 |
High resolution limit [Å] | 1.800 | 1.800 |
Rmerge | 0.135 | 0.952 |
Rmeas | 0.148 | 1.115 |
Rpim | 0.060 | 0.569 |
Number of reflections | 67386 | 6082 |
<I/σ(I)> | 9.62 | 1.99 |
Completeness [%] | 91.0 | 81.98 |
Redundancy | 5 | 3.3 |
CC(1/2) | 0.994 | 0.730 |
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. |