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SASDRL2 – Chicken Netrin-1 ΔC monomer (experiment ID: sm22113-7/sample11)

Netrin-1 experimental SAS data
Sample: Netrin-1 monomer, 50 kDa Gallus gallus protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 4.1 nm
Dmax 21.0 nm
VolumePorod 84 nm3

SASDRM2 – Chicken Netrin-1 ΔC dimer (experiment ID: sm22113-7/sample11)

Netrin-1 experimental SAS data
Sample: Netrin-1 dimer, 99 kDa Gallus gallus protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 5.8 nm
Dmax 23.0 nm
VolumePorod 142 nm3

SASDRN2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp8 (experiment ID: sm16028-7/379532)

Netrin-1Heparin oligosaccharide dp8 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp8 ammonium salt monomer, 2 kDa Sus scrofa domesticus
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 6.5 nm
Dmax 23.5 nm
VolumePorod 729 nm3

SASDRP2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp8 (experiment ID: sm16028-7/379539)

Netrin-1Heparin oligosaccharide dp8 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp8 ammonium salt monomer, 2 kDa Sus scrofa domesticus
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 6.4 nm
Dmax 21.9 nm
VolumePorod 723 nm3

SASDRQ2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp10 (experiment ID: sm16028-7/379533)

Netrin-1Heparin oligosaccharide dp10 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp10 ammonium salt monomer, 3 kDa Sus scrofa domesticus
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 6.4 nm
Dmax 21.7 nm
VolumePorod 758 nm3

SASDRR2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp10 (experiment ID: sm16028-7/379540)

Netrin-1Heparin oligosaccharide dp10 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp10 ammonium salt monomer, 3 kDa Sus scrofa domesticus
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 6.5 nm
Dmax 21.9 nm
VolumePorod 769 nm3

SASDR36 – Pisum sativum Toc75 Potra domains

Protein TOC75, chloroplastic experimental SAS data
Protein TOC75, chloroplastic Kratky plot
Sample: Protein TOC75, chloroplastic monomer, 32 kDa Pisum sativum protein
Buffer: phosphate buffered saline, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 23
Characterization of synthetic antigen binding fragments targeting Toc75 for the isolation of TOC in A. thaliana and P. sativum Structure (2023)
Srinivasan K, Erramilli S, Chakravarthy S, Gonzalez A, Kossiakoff A, Noinaj N
RgGuinier 2.9 nm
Dmax 11.0 nm
VolumePorod 60 nm3

SASDP74 – AT-rich DNA

AT-rich dsDNA experimental SAS data
DAMMIN model
Sample: AT-rich dsDNA monomer, 7 kDa DNA
Buffer: 20 mM Tris-HCl, pH 7.5, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Feb 6
Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome. Life Sci Alliance 6(3) (2023)
Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG
RgGuinier 1.7 nm
Dmax 4.6 nm
VolumePorod 12 nm3

SASDPZ8 – Gli-233 - ssDNA aptamer specific to glioma brain tumor cells

Gli-233 - ssDNA aptamer to glioma brain tumor cells experimental SAS data
GROMACS model
Sample: Gli-233 - ssDNA aptamer to glioma brain tumor cells monomer, 10 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS, with Ca and Mg), pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 17
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M
RgGuinier 1.9 nm
Dmax 6.8 nm
VolumePorod 13 nm3

SASDP29 – Gli-55 - ssDNA aptamer specific to glioma brain tumor cells

Gli-55 - ssDNA aptamer specific to glioma brain tumor cells experimental SAS data
DAMMIN model
Sample: Gli-55 - ssDNA aptamer specific to glioma brain tumor cells monomer, 19 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS), pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Oct 30
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M
RgGuinier 2.8 nm
Dmax 11.5 nm
VolumePorod 34 nm3