8A4W
Crystal structure of human cathepsin L with covalently bound Cathepsin L inhibitor IV
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 | 57.310, 62.580, 68.160 |
Unit cell angles | 105.67, 93.33, 115.30 |
Refinement procedure
Resolution | 44.390 - 1.400 |
R-factor | 0.1455 |
Rwork | 0.145 |
R-free | 0.16670 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3of9 |
RMSD bond length | 0.007 |
RMSD bond angle | 0.827 |
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] | 44.390 | 1.450 |
High resolution limit [Å] | 1.400 | 1.400 |
Rmerge | 0.195 | 2.080 |
Rmeas | 0.203 | 2.202 |
Rpim | 0.055 | 0.706 |
Number of reflections | 146390 | 9238 |
<I/σ(I)> | 11.18 | 1.7 |
Completeness [%] | 91.9 | 57.71 |
Redundancy | 13.1 | 9.1 |
CC(1/2) | 0.998 | 0.454 |
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. |