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Linear specific OTU-type DUB SnOTU from the pathogen S. negenvensis in complex with linear di-ubiquitin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Prediction of the crystallized fragment
Crystallization
Crystalization Experiments
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.
Crystal Properties
Matthews coefficient
Solvent content
2.77
55.66
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 154.618
α = 90
b = 154.618
β = 90
c = 81.972
γ = 120
Symmetry
Space Group
P 61
Diffraction
Diffraction Experiment
ID #
Crystal ID
Scattering Type
Data Collection Temperature
Detector
Detector Type
Details
Collection Date
Monochromator
Protocol
1
1
x-ray
100
PIXEL
DECTRIS EIGER X 16M
2021-12-16
M
SINGLE WAVELENGTH
Radiation Source
ID #
Source
Type
Wavelength List
Synchrotron Site
Beamline
1
SYNCHROTRON
PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
1.00000
PETRA III, EMBL c/o DESY
P13 (MX1)
Data Collection
Overall
ID #
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
Rrim I (All)
Rpim I (All)
CC (Half)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
1
2.24
80
99.9
0.134
0.1406
0.0417
0.997
8.9
11.2
53800
57.15
Highest Resolution Shell
ID #
Resolution (High)
Resolution (Low)
Percent Possible (All)
Percent Possible (Observed)
R Merge I (Observed)
Rrim I (All)
Rpim I (All)
CC (Half)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
1
2.24
2.32
99.6
1.972
2.072
0.6039
0.643
11.7
Refinement
Statistics
Diffraction ID
Structure Solution Method
Cross Validation method
Starting model
Resolution (High)
Resolution (Low)
Cut-off Sigma (F)
Number Reflections (Observed)
Number Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (Observed)
R-Work (Depositor)
R-Work (DCC)
R-Free (Depositor)
R-Free (DCC)
R-Free Selection Details
Mean Isotropic B
X-RAY DIFFRACTION
MOLECULAR REPLACEMENT
FREE R-VALUE
AlphaFold2; custom version (https://github.com/muthoff/ComplexFold)