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.