8CMR
Linear specific OTU-type DUB SnOTU from the pathogen S. negenvensis in complex with linear di-ubiquitin
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-12-16 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.00000 |
Spacegroup name | P 61 |
Unit cell lengths | 154.618, 154.618, 81.972 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 43.060 - 2.240 |
R-factor | 0.1946 |
Rwork | 0.194 |
R-free | 0.21450 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | AlphaFold2; custom version (https://github.com/muthoff/ComplexFold) |
RMSD bond length | 0.002 |
RMSD bond angle | 0.472 |
Data reduction software | XDS (Feb 5, 2021 BUILT=20210323) |
Data scaling software | XSCALE (Feb 5, 2021 BUILT=20210323) |
Phasing software | PHASER (2.8.3) |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 80.000 | 2.320 |
High resolution limit [Å] | 2.240 | 2.240 |
Rmerge | 0.134 | 1.972 |
Rmeas | 0.141 | 2.072 |
Rpim | 0.042 | 0.604 |
Number of reflections | 53800 | 5272 |
<I/σ(I)> | 8.9 | |
Completeness [%] | 99.9 | 99.6 |
Redundancy | 11.2 | 11.7 |
CC(1/2) | 0.997 | 0.643 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | The proteins were purified in 20 mM TRIS pH 7.5, 150 mM NaCl, 2mM DTT and mixed in a 1:1.1 (Protease:ubiquitin) ratio. Reservoir: 0.2 M Magnesium format dihydrate, 20 % w/v PEG 3350, 0.02 M EDTA Protein and reservoir were mixed in a ratio of 1 ul : 2 ul. |