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53 hits found for Jeffries

SASDC22 – Tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7

Homeobox protein CEH-14CeLIM-7 experimental SAS data
DAMMIN model
Sample: Homeobox protein CEH-14 monomer, 16 kDa Caenorhabditis elegans protein
CeLIM-7 monomer, 4 kDa Caenorhabditis elegans protein
Buffer: 50 mM Tris, 100 mM NaCl, 5 mM TCEP, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSess, University of Sydney on 2009 Apr 7
Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans. Sci Rep 7(1):4579 (2017)
...Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM
RgGuinier 2.4 nm
Dmax 8.9 nm
VolumePorod 26 nm3

SASDD32 – DNA-(adenine N6)-methyltransferase from Acinetobacter baumannii ATCC 17978

DNA-(adenine N6)-methyltransferase experimental SAS data
DAMMIN model
Sample: DNA-(adenine N6)-methyltransferase monomer, 49 kDa Acinetobacter baumannii protein
Buffer: 150mM NaCl, 10mM Tris, 1mM DTT, 5% v/v glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 30
Recombinant production of A1S_0222 from Acinetobacter baumannii ATCC 17978 and confirmation of its DNA-(adenine N6)-methyltransferase activity. Protein Expr Purif 151:78-85 (2018)
...Jeffries CM, Svergun DI, Wilharm G
RgGuinier 2.9 nm
Dmax 11.1 nm
VolumePorod 96 nm3

SASDD42 – Synechocystis fluorescence recovery protein SynFRP.8-109

Fluorescence recovery protein experimental SAS data
GASBOR model
Sample: Fluorescence recovery protein dimer, 23 kDa Synechocystis sp. PCC … protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, 0.1 mM EDTA, 2 mM dithiothreitol, 3 % v/v glycerol, pH: 7.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Sep 1
Functional interaction of low-homology FRPs from different cyanobacteria with Synechocystis OCP. Biochim Biophys Acta 1859(5):382-393 (2018)
...Jeffries CM, Svergun DI, Friedrich T, Sluchanko NN
RgGuinier 2.8 nm
Dmax 10.5 nm
VolumePorod 36 nm3

SASDD52 – Arthrospira fluorescence recovery protein AmaxFRP.1-106

Uncharacterized fluorescence recovery protein experimental SAS data
GASBOR model
Sample: Uncharacterized fluorescence recovery protein dimer, 24 kDa Arthrospira maxima CS-328 protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, 0.1 mM EDTA, 2 mM dithiothreitol, 3 % v/v glycerol, pH: 7.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Sep 1
Functional interaction of low-homology FRPs from different cyanobacteria with Synechocystis OCP. Biochim Biophys Acta 1859(5):382-393 (2018)
...Jeffries CM, Svergun DI, Friedrich T, Sluchanko NN
RgGuinier 2.7 nm
Dmax 9.5 nm
VolumePorod 35 nm3

SASDH92 – Plasmodium falciparum lipocalin (PF3D7_0925900): Dimer-tetramer equilibrium through a concentration series (combined batch and SEC-SAXS measurements)

Plasmodium falciparum Lipocalin experimental SAS data
SASREF MX model
Sample: Plasmodium falciparum Lipocalin tetramer, 89 kDa Plasmodium falciparum protein
Buffer: 20 mM Tris pH7.5, 150 mM NaCl, 5% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 8
Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum Cell Reports 31(12):107817 (2020)
...Jeffries C, Svergun D, Wilson D, Wilmanns M, Gilberger T
RgGuinier 3.2 nm
Dmax 10.3 nm
VolumePorod 126 nm3

SASDAB2 – Cytochrome c from equine heart

Cytochrome cHeme C experimental SAS data
PDB model
Sample: Cytochrome c monomer, 12 kDa Equus caballus protein
Heme C monomer, 1 kDa
Buffer: 25 mM HEPES, 100 mM NaCl, 3% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Apr 8
Standard proteins
Cy M Jeffries
RgGuinier 1.3 nm
Dmax 3.7 nm
VolumePorod 12 nm3

SASDBR2 – Contactin-associated protein-like 2 (Caspr2) extracellular domains 1-1261.

Contactin-associated protein-like 2 extracellular domains (1-1261) experimental SAS data
DAMMIN model
Sample: Contactin-associated protein-like 2 extracellular domains (1-1261) monomer, 140 kDa Homo sapiens protein
Buffer: 10 mM HEPES 150 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Anton Paar SAXSess, University of Utah on 2010 Oct 4
Structural Characterization of the Extracellular Domain of CASPR2 and Insights into Its Association with the Novel Ligand Contactin1. J Biol Chem 291(11):5788-802 (2016)
...Jeffries CM, Shaikh TR, Pakos IS, Ranaivoson FM, von Daake S, Demeler B, De Jaco A, Perkins G, Ellisman MH, Trewhella J, Comoletti D
RgGuinier 4.4 nm
Dmax 14.5 nm
VolumePorod 282 nm3

SASDBY2 – Inorganic pyrophosphatase (PPase) from E. coli

Inorganic pyrophosphatase (PPase) from E. coli experimental SAS data
DAMMIN model
Sample: Inorganic pyrophosphatase (PPase) from E. coli hexamer, 117 kDa Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 30
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
...Jeffries CM, Svergun DI
RgGuinier 3.0 nm
Dmax 9.0 nm
VolumePorod 166 nm3

SASDBZ2 – Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli experimental SAS data
DAMMIN model
Sample: Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli decamer, 381 kDa Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 30
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
...Jeffries CM, Svergun DI
RgGuinier 4.4 nm
Dmax 12.7 nm
VolumePorod 484 nm3

SASDB23 – 5-keto-4-deoxyuronate isomerase (KduI) from E. coli

5-keto-4-deoxyuronate isomerase (KduI) from E. coli experimental SAS data
NONE model
Sample: 5-keto-4-deoxyuronate isomerase (KduI) from E. coli None, Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 20
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
...Jeffries CM, Svergun DI
RgGuinier 4.5 nm

SASDB33 – Glutamate decarboxylase alpha (GadA) from E. coli

Glutamate decarboxylase alpha (GadA) from E. coli experimental SAS data
SASREF MX model
Sample: Glutamate decarboxylase alpha (GadA) from E. coli monomer, 53 kDa Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 20
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
...Jeffries CM, Svergun DI
RgGuinier 4.8 nm
VolumePorod 410 nm3

SASDH43 – N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 (IP3RN)

N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 experimental SAS data
BUNCH model
Sample: N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 monomer, 70 kDa Mus musculus protein
Buffer: 15 mM Tris, 300 mM NaCl, 1 mM TCEP, 5 mM EGTA, pH: 8
Experiment: SAXS data collected at Bruker Nanostar II, Australian Nuclear Science and Technology Organisation/Australian Centre for Neutron Scattering on 2006 Apr 12
Ligand-induced conformational changes via flexible linkers in the amino-terminal region of the inositol 1,4,5-trisphosphate receptor. J Mol Biol 373(5):1269-80 (2007)
...Jeffries CM, Bosanac I, Mal TK, Ito J, Porumb H, Michikawa T, Mikoshiba K, Trewhella J, Ikura M
RgGuinier 3.2 nm
Dmax 10.0 nm
VolumePorod 135 nm3

SASDH53 – N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 (IP3RN) with calcium

N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 experimental SAS data
BUNCH model
Sample: N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 monomer, 70 kDa Mus musculus protein
Buffer: 15 mM Tris, 300 mM NaCl, 1 mM TCEP, 10 mM CaCl2, pH: 8
Experiment: SAXS data collected at Bruker Nanostar II, Australian Nuclear Science and Technology Organisation/Australian Centre for Neutron Scattering on 2006 Apr 12
Ligand-induced conformational changes via flexible linkers in the amino-terminal region of the inositol 1,4,5-trisphosphate receptor. J Mol Biol 373(5):1269-80 (2007)
...Jeffries CM, Bosanac I, Mal TK, Ito J, Porumb H, Michikawa T, Mikoshiba K, Trewhella J, Ikura M
RgGuinier 3.4 nm
Dmax 11.0 nm
VolumePorod 160 nm3

SASDH63 – N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 (IP3RN) with bound inositol 1,4,5-trisphosphate (IP3)

N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 experimental SAS data
BUNCH model
Sample: N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 monomer, 70 kDa Mus musculus protein
Buffer: 15 mM Tris, 300 mM NaCl, 1 mM TCEP, 5 mM EGTA, 0.25 mM IP3, pH: 8
Experiment: SAXS data collected at Bruker Nanostar II, Australian Nuclear Science and Technology Organisation/Australian Centre for Neutron Scattering on 2006 Apr 12
Ligand-induced conformational changes via flexible linkers in the amino-terminal region of the inositol 1,4,5-trisphosphate receptor. J Mol Biol 373(5):1269-80 (2007)
...Jeffries CM, Bosanac I, Mal TK, Ito J, Porumb H, Michikawa T, Mikoshiba K, Trewhella J, Ikura M
RgGuinier 3.1 nm
Dmax 8.8 nm
VolumePorod 115 nm3

SASDH73 – N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 (IP3RN) with bound inositol 1,4,5-trisphosphate (IP3) plus calcium

N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 experimental SAS data
BUNCH model
Sample: N-terminal domains of the inositol 1,4,5-trisphosphate receptor type 1 monomer, 70 kDa Mus musculus protein
Buffer: 15 mM Tris, 300 mM NaCl, 1 mM TCEP, 10 mM CaCl2, 0.25 mM IP3, pH: 8
Experiment: SAXS data collected at Bruker Nanostar II, Australian Nuclear Science and Technology Organisation/Australian Centre for Neutron Scattering on 2006 Apr 12
Ligand-induced conformational changes via flexible linkers in the amino-terminal region of the inositol 1,4,5-trisphosphate receptor. J Mol Biol 373(5):1269-80 (2007)
...Jeffries CM, Bosanac I, Mal TK, Ito J, Porumb H, Michikawa T, Mikoshiba K, Trewhella J, Ikura M
RgGuinier 3.2 nm
Dmax 9.6 nm
VolumePorod 132 nm3

SASDBJ3 – Bovine serum albumin, monomer from SEC-SAXS

Bovine serum albumin, monomer experimental SAS data
PDB model
Sample: Bovine serum albumin, monomer monomer, 66 kDa Bos taurus protein
Buffer: 25 mM Tris 150 mM NaCl 3% (v/v) glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 23
Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 11(11):2122-2153 (2016)
Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI
RgGuinier 2.8 nm
Dmax 8.2 nm
VolumePorod 100 nm3

SASDDJ3 – Candida antarctica lipase B - with guanidine-HCl unfolding series

Lipase B from Pseudozyma antarctica experimental SAS data
Lipase B from Pseudozyma antarctica Kratky plot
Sample: Lipase B from Pseudozyma antarctica , 33 kDa Moesziomyces antarcticus protein
Buffer: 100 mM NaCl, 20 mM Na2HPO4, pH: 6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jul 29
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. Biophys J 114(11):2485-2492 (2018)
...Jeffries CM, Svergun DI
RgGuinier 2.4 nm

SASDBK3 – Bovine serum albumin, dimer from SEC-SAXS

Bovine serum albumin, dimer experimental SAS data
PDB model
Sample: Bovine serum albumin, dimer dimer, 133 kDa Bos taurus protein
Buffer: 25 mM Tris 150 mM NaCl 3% (v/v) glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 23
Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 11(11):2122-2153 (2016)
Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI
RgGuinier 3.9 nm
Dmax 12.7 nm
VolumePorod 202 nm3

SASDDK3 – Candida antarctica lipase B - with guanidine-HCl unfolding series, in the presence of dithiothreitol

Lipase B from Pseudozyma antarctica experimental SAS data
Lipase B from Pseudozyma antarctica Kratky plot
Sample: Lipase B from Pseudozyma antarctica , 33 kDa Moesziomyces antarcticus protein
Buffer: 100 mM NaCl, 20 mM Na2HPO4, 10 mM DTT, pH: 6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jul 29
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. Biophys J 114(11):2485-2492 (2018)
...Jeffries CM, Svergun DI
RgGuinier 2.4 nm

SASDDL3 – Folded ribonuclease A (RNAse)

Ribonuclease pancreatic experimental SAS data
PDB model
Sample: Ribonuclease pancreatic monomer, 16 kDa Bos taurus protein
Buffer: phosphate buffered saline (PBS), pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jul 29
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. Biophys J 114(11):2485-2492 (2018)
...Jeffries CM, Svergun DI
RgGuinier 1.6 nm
Dmax 5.6 nm
VolumePorod 16 nm3

SASDDM3 – Carboyxamidomethylated ribonuclease A (unfolded RNAse) - with and without urea

Ribonuclease pancreatic experimental SAS data
Ribonuclease pancreatic Kratky plot
Sample: Ribonuclease pancreatic monomer, 16 kDa Bos taurus protein
Buffer: 10 mM HCl, pH: 1
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jul 29
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. Biophys J 114(11):2485-2492 (2018)
...Jeffries CM, Svergun DI
RgGuinier 2.3 nm
Dmax 9.0 nm

SASDDN3 – Bovine serum albumin mixture: averaged and individual data frames (subtracted and unsubtracted test sets)

Bovine serum albumin experimental SAS data
Bovine serum albumin Kratky plot
Sample: Bovine serum albumin , 66 kDa Bos taurus protein
Buffer: 50 mM HEPES, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 25
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. Biophys J 114(11):2485-2492 (2018)
...Jeffries CM, Svergun DI
RgGuinier 3.0 nm
Dmax 11.0 nm
VolumePorod 117 nm3

SASDF94 – Insulin glulisine (Apidra), oligomeric composition

Insulin glulisine experimental SAS data
CUSTOM IN-HOUSE model
Sample: Insulin glulisine hexamer, 35 kDa protein
Buffer: Apidra formulation (per ml: 5 mg Sodium chloride, 3.15 mg m-Cresol, 6 mg Trometamol, 0.01 mg Polysorbate 20), pH: 7.3
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Apr 20
The quaternary structure of insulin glargine and glulisine under formulation conditions. Biophys Chem 253:106226 (2019)
...Jeffries CM, Svergun D, Berchtold H
RgGuinier 2.3 nm
Dmax 7.6 nm

SASDFA4 – Insulin glargine (Toujeo®), oligomeric composition

Insulin glargine (Toujeo®) experimental SAS data
PDB model
Sample: Insulin glargine (Toujeo®) hexamer, 36 kDa protein
Buffer: Toujeo Fromulation (190 ug Zinc chloride, 2.7 mg m-Cresol, 20 mg glycerol 85%), pH: 4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 5
The quaternary structure of insulin glargine and glulisine under formulation conditions. Biophys Chem 253:106226 (2019)
...Jeffries CM, Svergun D, Berchtold H
RgGuinier 1.8 nm
Dmax 6.2 nm

SASDFB4 – Insulin glargine (Lantus ®), oligomeric mixture

Insulin glargine (Lantus ®) experimental SAS data
Insulin glargine (Lantus ®) Kratky plot
Sample: Insulin glargine (Lantus ®) hexamer, 36 kDa protein
Buffer: Lantus Formulation (30 µg Zinc cloride, 2.7 mg m-Cresol, 20 mg glycerol 85%), pH: 4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 May 23
The quaternary structure of insulin glargine and glulisine under formulation conditions. Biophys Chem 253:106226 (2019)
...Jeffries CM, Svergun D, Berchtold H
RgGuinier 1.8 nm
Dmax 5.3 nm

SASDJF4 – Synthetic nanobody Sybody 23 (Sy23)

Synthetic nanobody Sybody 23 experimental SAS data
CORAL model
Sample: Synthetic nanobody Sybody 23 monomer, 16 kDa synthetic construct protein
Buffer: 50 mM Tris 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 May 5
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 (2020)
...Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C
RgGuinier 2.1 nm
Dmax 8.0 nm
VolumePorod 22 nm3

SASDJG4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD)

Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data
SASREF model
Sample: Spike glycoprotein (ACE2 receptor binding domain) monomer, 29 kDa Severe acute respiratory … protein
Buffer: 25 mM Tris 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 May 1
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 (2020)
...Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C
RgGuinier 3.0 nm
Dmax 13.1 nm
VolumePorod 64 nm3

SASDJH4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23)

Synthetic nanobody Sybody 23Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data
CORAL model
Sample: Synthetic nanobody Sybody 23 monomer, 16 kDa synthetic construct protein
Spike glycoprotein (ACE2 receptor binding domain) monomer, 29 kDa Severe acute respiratory … protein
Buffer: 25 mM Tris 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 May 10
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 (2020)
...Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C
RgGuinier 3.5 nm
Dmax 15.1 nm
VolumePorod 87 nm3

SASDBS4 – Glutamate decarboxylase alpha (GadA) from E. coli, low salt

Glutamate decarboxylase alpha (GadA) from E. coli experimental SAS data
SASREF MX model
Sample: Glutamate decarboxylase alpha (GadA) from E. coli monomer, 53 kDa Escherichia coli protein
Buffer: 50 mM Tris, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jul 29
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
...Jeffries CM, Svergun DI
RgGuinier 4.4 nm
VolumePorod 450 nm3

SASDB95 – Shigella outer membrane protein IcsA autotransporter

Outer membrane protein IcsA (53-758) experimental SAS data
DAMMIN model
Sample: Outer membrane protein IcsA (53-758) monomer, 72 kDa Shigella flexneri protein
Buffer: 50 mM Tris 150 mM NaCl 10 mM CaCl2 3% v/v glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 May 18
The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain. J Biol Chem 292(1):134-145 (2017)
...Jeffries CM, Svergun DI, Deane JE
RgGuinier 3.7 nm
Dmax 13.2 nm
VolumePorod 103 nm3

SASDAL5 – Clostridium difficile bacteriophage 27 endolysin dimer, CD27L

Clostridium difficile bacteriophage 27 endolysin experimental SAS data
NONE model
Sample: Clostridium difficile bacteriophage 27 endolysin dimer, 64 kDa Clostridioides difficile protein
Buffer: 20 mM HEPES 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III on 2011 Mar 17
The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLoS Pathog 10(7):e1004228 (2014)
...Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A, Meijers R
RgGuinier 3.3 nm
Dmax 10.6 nm
VolumePorod 72 nm3

SASDAM5 – Clostridium difficile bacteriophage 27 endolysin dimer C238R mutant, CD27L-C238R

Clostridium difficile bacteriophage 27 endolysin C238R mutant experimental SAS data
DAMMIF model
Sample: Clostridium difficile bacteriophage 27 endolysin C238R mutant dimer, 64 kDa Clostridioides difficile protein
Buffer: 20 mM HEPES 500 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 21
The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLoS Pathog 10(7):e1004228 (2014)
...Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A, Meijers R
RgGuinier 4.2 nm
Dmax 14.7 nm
VolumePorod 92 nm3

SASDA96 – Lysozyme

Lysozyme C experimental SAS data
DAMMIF model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 20 mM Sodium Acetate/HEPES, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Feb 17
Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra. Nat Methods 12(5):419-22 (2015)
...Jeffries CM, Svergun DI
RgGuinier 1.5 nm
Dmax 4.8 nm
VolumePorod 24 nm3

SASDAA6 – Human serum albumin monomer and mixtures

Human serum albumin monomer experimental SAS data
DAMMIF model
Sample: Human serum albumin monomer monomer, 66 kDa Homo sapiens protein
Buffer: 50 mM HEPES, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 22
Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra. Nat Methods 12(5):419-22 (2015)
...Jeffries CM, Svergun DI
RgGuinier 2.8 nm
Dmax 8.4 nm
VolumePorod 103 nm3

SASDAB6 – Xylose Isomerase

Xylose Isomerase experimental SAS data
DAMMIF model
Sample: Xylose Isomerase tetramer, 173 kDa Streptomyces rubiginosus protein
Buffer: 20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2, pH: 6.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 10
Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra. Nat Methods 12(5):419-22 (2015)
...Jeffries CM, Svergun DI
RgGuinier 3.2 nm
Dmax 9.1 nm
VolumePorod 234 nm3

SASDAF6 – K1K2K3 domain of Kgp gingipain

K1K2K3 adhesin modules of lysine-specific (Kgp) gingipain experimental SAS data
BUNCH model
Sample: K1K2K3 adhesin modules of lysine-specific (Kgp) gingipain monomer, 74 kDa Porphyromonas gingivalis W83 protein
Buffer: 10 mM TRIS 150 mM NaCl, pH: 7.6
Experiment: SAXS data collected at Anton Paar SAXSess, University of Sydney on 2010 Aug 15
The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis. Mol Microbiol 81(5):1358-73 (2011)
...Jeffries CM, Langley D, Gamsjaeger R, Church WB, Hunter N, Collyer CA
RgGuinier 4.3 nm
Dmax 14.7 nm

SASDAG6 – K1K2 domains of Kgp gingipain

K1K2 adhesin modules of lysine-specific (Kgp) gingipain experimental SAS data
BUNCH model
Sample: K1K2 adhesin modules of lysine-specific (Kgp) gingipain monomer, 38 kDa Porphyromonas gingivalis W83 protein
Buffer: 10 mM TRIS 150 mM NaCl, pH: 7.6
Experiment: SAXS data collected at Anton Paar SAXSess, University of Sydney on 2010 Aug 15
The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis. Mol Microbiol 81(5):1358-73 (2011)
...Jeffries CM, Langley D, Gamsjaeger R, Church WB, Hunter N, Collyer CA
RgGuinier 2.9 nm
Dmax 9.5 nm

SASDA37 – Surface Protein G (SasG) EG5 repeat protein G51-G52

Surface protein G experimental SAS data
SASREF model
Sample: Surface protein G monomer, 24 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris 200 mM NaCl 1 mM EDTA 20 mM Tris.Cl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 12
Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nat Commun 6:7271 (2015)
...Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J
RgGuinier 4.7 nm
Dmax 19.0 nm
VolumePorod 29 nm3

SASDG37 – 1:2 heterotrimer of pUL7 and pUL51(8-142) from herpes simplex virus 1

Tegument protein UL7Tegument protein UL51 experimental SAS data
DAMMIN model
Sample: Tegument protein UL7 monomer, 34 kDa Human alphaherpesvirus 1 … protein
Tegument protein UL51 dimer, 30 kDa Human alphaherpesvirus 1 … protein
Buffer: 20 mM tris, 200 mM NaCl, 3% (v/v) glycerol, 0.25 mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 May 16
Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex. Elife 9 (2020)
...Jeffries CM, Ivanova L, Hill CH, Houghton JW, Ahmed MF, Antrobus R, Svergun DI, Welch JJ, Crump CM, Graham SC
RgGuinier 3.0 nm
Dmax 11.5 nm
VolumePorod 116 nm3

SASDA47 – Surface Protein G (SasG) EG5 repeat protein G51-G53

Surface protein G experimental SAS data
SASREF model
Sample: Surface protein G monomer, 39 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris 200 mM NaCl 1 mM EDTA 20 mM Tris.Cl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 12
Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nat Commun 6:7271 (2015)
...Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J
RgGuinier 7.7 nm
Dmax 30.5 nm
VolumePorod 49 nm3

SASDG47 – 2:4 heterohexamer of pUL7 and pUL51 from herpes simplex virus 1

Tegument protein UL7Tegument protein UL51 experimental SAS data
DAMMIN model
Sample: Tegument protein UL7 dimer, 68 kDa Human alphaherpesvirus 1 … protein
Tegument protein UL51 tetramer, 102 kDa Human alphaherpesvirus 1 … protein
Buffer: 20 mM HEPES, 200 mM NaCl, 3% (v/v) glycerol, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 May 16
Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex. Elife 9 (2020)
...Jeffries CM, Ivanova L, Hill CH, Houghton JW, Ahmed MF, Antrobus R, Svergun DI, Welch JJ, Crump CM, Graham SC
RgGuinier 4.6 nm
Dmax 19.7 nm
VolumePorod 340 nm3

SASDA57 – Surface Protein G (SasG) EG5 repeat protein G51-G54

Surface protein G experimental SAS data
GASBOR model
Sample: Surface protein G monomer, 53 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris 200 mM NaCl 1 mM EDTA 20 mM Tris.Cl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 12
Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nat Commun 6:7271 (2015)
...Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J
RgGuinier 9.7 nm
Dmax 38.5 nm
VolumePorod 58 nm3

SASDG57 – 1:2 heterotrimer of pUL7 and pUL51 from herpes simplex virus 1

Tegument protein UL7Tegument protein UL51 experimental SAS data
GASBOR model
Sample: Tegument protein UL7 monomer, 34 kDa Human alphaherpesvirus 1 … protein
Tegument protein UL51 dimer, 51 kDa Human alphaherpesvirus 1 protein
Buffer: 20 mM HEPES, 200 mM NaCl, 3% (v/v) glycerol, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 May 16
Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex. Elife 9 (2020)
...Jeffries CM, Ivanova L, Hill CH, Houghton JW, Ahmed MF, Antrobus R, Svergun DI, Welch JJ, Crump CM, Graham SC
RgGuinier 4.0 nm
Dmax 18.2 nm
VolumePorod 160 nm3

SASDA67 – Surface Protein G (SasG) EG5 repeat protein G51-G55

Surface protein G experimental SAS data
SASREF model
Sample: Surface protein G monomer, 67 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris 200 mM NaCl 1 mM EDTA 20 mM Tris.Cl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 12
Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nat Commun 6:7271 (2015)
...Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J
RgGuinier 12.0 nm
Dmax 48.0 nm
VolumePorod 87 nm3

SASDA77 – Surface Protein G (SasG) EG5 repeat protein G51-G56

Surface protein G experimental SAS data
SASREF model
Sample: Surface protein G monomer, 81 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris 200 mM NaCl 1 mM EDTA 20 mM Tris.Cl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 12
Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nat Commun 6:7271 (2015)
...Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J
RgGuinier 14.1 nm
Dmax 57.0 nm
VolumePorod 89 nm3

SASDA87 – Surface Protein G (SasG) EG5 repeat protein G51-G57

Surface protein G experimental SAS data
SASREF model
Sample: Surface protein G monomer, 95 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris 200 mM NaCl 1 mM EDTA 20 mM Tris.Cl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 12
Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nat Commun 6:7271 (2015)
...Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J
RgGuinier 15.9 nm
Dmax 63.0 nm
VolumePorod 122 nm3

SASDA97 – PlaB

PlaB experimental SAS data
DAMMIN model
Sample: PlaB tetramer, 220 kDa Legionella pneumophila protein
Buffer: 100 mM Tris 100 mM Nacl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 15
Automated pipeline for purification, biophysical and x-ray analysis of biomacromolecular solutions. Sci Rep 5:10734 (2015)
...Jeffries CM, Blanchet CE, Ruskule D, Kuhle K, Flieger A, Schäfer B, Tartsch B, Meijers R, Svergun DI
RgGuinier 4.0 nm
Dmax 10.5 nm
VolumePorod 270 nm3

SASDFN8 – Apoferritin from horse spleen - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Apoferritin light chain experimental SAS data
DAMMIN model
Sample: Apoferritin light chain 24-mer, 479 kDa Equus caballus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
SASBDB Standard Proteins
Melissa Graewert, Cy M Jeffries
RgGuinier 5.4 nm
Dmax 12.5 nm
VolumePorod 679 nm3

SASDFP8 – Carbonic anhydrase 2 from bovine erythrocytes - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Carbonic anhydrase 2 experimental SAS data
DAMMIN model
Sample: Carbonic anhydrase 2 monomer, 29 kDa Bos taurus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
SASBDB Standard Proteins
Melissa Graewert, Cy M Jeffries
RgGuinier 1.8 nm
Dmax 5.1 nm
VolumePorod 37 nm3

SASDFQ8 – Bovine serum albumin, purified monomer - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Bovine serum albumin experimental SAS data
GASBOR model
Sample: Bovine serum albumin monomer, 66 kDa Bos taurus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
SASBDB Standard Proteins
Melissa Graewert, Cy M Jeffries
RgGuinier 2.8 nm
Dmax 8.0 nm
VolumePorod 98 nm3

SASDFR8 – Bovine serum albumin, purified dimer - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Bovine serum albumin experimental SAS data
GASBOR model
Sample: Bovine serum albumin dimer, 133 kDa Bos taurus protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
SASBDB Standard Proteins
Melissa Graewert, Cy M Jeffries
RgGuinier 4.0 nm
Dmax 13.2 nm
VolumePorod 211 nm3

SASDFS8 – Yeast alcohol dehydrogenase 1 - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Alcohol dehydrogenase 1 experimental SAS data
DAMMIN model
Sample: Alcohol dehydrogenase 1 tetramer, 147 kDa Saccharomyces cerevisiae protein
Buffer: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 5
SASBDB Standard Proteins
Melissa Graewert, Cy M Jeffries
RgGuinier 3.3 nm
Dmax 9.3 nm
VolumePorod 201 nm3

SASDF99 – Bovine serum albumin monomer - SEC-SAXS/WAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

Bovine serum albumin experimental SAS data
GASBOR model
Sample: Bovine serum albumin monomer, 66 kDa Bos taurus protein
Buffer: 50 mM HEPES, 3% v/v glycerol,, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Apr 23
SASBDB Standard Proteins
Melissa Graewert, Cy M Jeffries
RgGuinier 2.8 nm
Dmax 8.3 nm
VolumePorod 95 nm3