Browse by MODEL: Ab initio only

SASDNM7 – Protease 1 from Pyrococcus horikoshii (PhP1) in Gd-HPDO3A

Deglycase PH1704 experimental SAS data
OTHER model
Sample: Deglycase PH1704 hexamer, 112 kDa Pyrococcus horikoshii (strain … protein
Buffer: 20 mM Tris pH 7.5, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2016 Jun 7
Medical contrast agents as promising tools for biomacromolecular SAXS experiments. Acta Crystallogr D Struct Biol 78(Pt 9):1120-1130 (2022)
Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E
RgGuinier 3.2 nm
Dmax 9.2 nm
VolumePorod 140 nm3

SASDNN7 – Protease 1 from Pyrococcus horikoshii (PhP1) in iohexol

Deglycase PH1704 experimental SAS data
OTHER model
Sample: Deglycase PH1704 hexamer, 112 kDa Pyrococcus horikoshii (strain … protein
Buffer: 20 mM Tris pH 7.5 and 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2016 Nov 26
Medical contrast agents as promising tools for biomacromolecular SAXS experiments. Acta Crystallogr D Struct Biol 78(Pt 9):1120-1130 (2022)
Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E
RgGuinier 3.2 nm
Dmax 9.2 nm
VolumePorod 140 nm3

SASDPA4 – SAXS data for the trimeric C-phycocyanin

C-phycocyanin alpha subunitC-phycocyanin beta subunit experimental SAS data
GASBOR model
Sample: C-phycocyanin alpha subunit trimer, 53 kDa Arthrospira platensis protein
C-phycocyanin beta subunit trimer, 54 kDa Arthrospira platensis protein
Buffer: 150 mM NaCl, 20 mM Tris, pH: 7.6
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2022 Apr 14
Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores Structural Dynamics 9(5):054701 (2022)
Tsoraev G, Protasova E, Klimanova E, Ryzhykau Y, Kuklin A, Semenov Y, Ge B, Li W, Qin S, Friedrich T, Sluchanko N, Maksimov E
RgGuinier 3.9 nm
Dmax 13.2 nm
VolumePorod 154 nm3

SASDPB4 – SAXS data for the C-phycocyanin in 8 M urea solution

C-phycocyanin alpha subunitC-phycocyanin beta subunit experimental SAS data
GASBOR model
Sample: C-phycocyanin alpha subunit monomer, 18 kDa Arthrospira platensis protein
C-phycocyanin beta subunit monomer, 18 kDa Arthrospira platensis protein
Buffer: 8 M urea, 30 mM βME, pH: 7
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2022 Apr 14
Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores Structural Dynamics 9(5):054701 (2022)
Tsoraev G, Protasova E, Klimanova E, Ryzhykau Y, Kuklin A, Semenov Y, Ge B, Li W, Qin S, Friedrich T, Sluchanko N, Maksimov E
RgGuinier 6.6 nm
Dmax 23.5 nm

SASDMV3 – Sigma-Aldrich polystyrene nanospheres with a diameter of 100 nm

Nominal 100 nm diameter polystyrene spheres experimental SAS data
BODIES model
Sample: Nominal 100 nm diameter polystyrene spheres monomer, 315312 kDa
Buffer: Water, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 May 16
Standard polystyrene nanospheres (concentration series data)
Dima Molodenskiy
RgGuinier 33.0 nm
Dmax 100.0 nm
VolumePorod 520 nm3

SASDMW3 – Thermo Fisher polystyrene nanospheres with a diameter of 20 nm

Nominal 20 nm diameter polystyrene spheres experimental SAS data
BODIES model
Sample: Nominal 20 nm diameter polystyrene spheres 0, 8 kDa
Buffer: Water, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 May 16
Standard polystyrene nanospheres (concentration series data)
Dima Molodenskiy
RgGuinier 8.5 nm
Dmax 25.0 nm
VolumePorod 3 nm3

SASDEX6 – Cold-active AMS8 lipase in the presence of calcium (without polyhistidine affinity tag)

LipAMS8 experimental SAS data
DAMMIF model
Sample: LipAMS8 monomer, 50 kDa Pseudomonas sp. AMS8 protein
Buffer: 50 mM Tris HCl, 5 mM CaCl2, pH: 8
Experiment: SAXS data collected at BL1.3W, Synchrotron Light Research Institute (SLRI) on 2018 Mar 6
Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD). Int J Biol Macromol (2022)
Yaacob N, Kamonsutthipaijit N, Soontaranon S, Leow TC, Rahman RNZRA, Ali MSM
RgGuinier 2.9 nm
Dmax 9.8 nm
VolumePorod 87 nm3

SASDN97 – Human thryoglobulin measured using SEC-SAXS

Thyroglobulin experimental SAS data
DAMMIN model
Sample: Thyroglobulin dimer, 610 kDa Homo sapiens protein
Buffer: phosphate buffered saline, 150mM NaCl, pH: 8
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2020 Jul 17
Thyroglobulin - human and bovine SAXS/WAXS data
James Byrnes
RgGuinier 7.7 nm
Dmax 26.3 nm
VolumePorod 1800 nm3

SASDNA7 – Bovine thyroglobulin in phosphate buffered saline/NaCl

Thyroglobulin experimental SAS data
DAMMIF model
Sample: Thyroglobulin dimer, 606 kDa Bos taurus protein
Buffer: phosphate buffered saline, 150mM NaCl, pH: 8
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2020 Jul 17
Thyroglobulin - human and bovine SAXS/WAXS data
James Byrnes
RgGuinier 8.1 nm
Dmax 29.8 nm
VolumePorod 1950 nm3

SASDJJ5 – Histone H2A:H2B:H3:H4 complex with aprataxin and polynucleotide kinase like factor (APLF) acidic domain

Aprataxin and PNK-like factor (acidic domain)Histone H2AHistone H2BHistone H3Histone H4 experimental SAS data
DAMMIF model
Sample: Aprataxin and PNK-like factor (acidic domain) dimer, 15 kDa Homo sapiens protein
Histone H2A dimer, 26 kDa Drosophila melanogaster protein
Histone H2B dimer, 27 kDa Drosophila melanogaster protein
Histone H3 dimer, 30 kDa Drosophila melanogaster protein
Histone H4 dimer, 23 kDa Drosophila melanogaster protein
Buffer: 25 mM NaPi, 300 mM NaCl, 3% v/v glycerol, 1 mM DTT,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Jul 10
Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv 8(30):eabo0517 (2022)
Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H
RgGuinier 3.7 nm
Dmax 10.8 nm
VolumePorod 260 nm3