Browse by MODEL: Ab initio only

SASDCT5 – SAXS on intact Doryteuthis squid lens 40% layer

S-crystallin, Q25367_DOROP experimental SAS data
DAMMIF model
Sample: S-crystallin, Q25367_DOROP dimer, 55 kDa Doryteuthis pealeii protein
Buffer: Tissue fluid, pH: 7
Experiment: SAXS data collected at X9A, National Synchrotron Light Source (NSLS) on 2014 Jul 17
Eye patches: Protein assembly of index-gradient squid lenses. Science 357(6351):564-569 (2017)
Cai J, Townsend JP, Dodson TC, Heiney PA, Sweeney AM

SASDCL2 – Tandem CBD from Clostridium histolyticum ColG collagenase at pCa 3

Class1 collagenase experimental SAS data
DAMMIF model
Sample: Class1 collagenase monomer, 27 kDa Hathewaya histolytica protein
Buffer: 10 mM HEPES 100 mM NaCL, 2% glycerol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 14
Structural characterization of bacterial collagenases University of Arkansas PhD thesis 2431 (2017)
Bauer R
RgGuinier 2.4 nm
Dmax 7.5 nm
VolumePorod 36 nm3

SASDCM2 – Tandem CBD from Clostridium histolyticum ColG collagenase at pCa 4

Class1 collagenase collagen-binding domain experimental SAS data
DAMMIF model
Sample: Class1 collagenase collagen-binding domain monomer, 27 kDa Hathewaya histolytica protein
Buffer: 10 mM HEPES 100 mM NaCL, 2% glycerol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 14
Structural characterization of bacterial collagenases University of Arkansas PhD thesis 2431 (2017)
Bauer R
RgGuinier 2.4 nm
Dmax 9.8 nm
VolumePorod 33 nm3

SASDCN2 – Tandem CBD from Clostridium histolyticum ColG collagenase at pCa 5

Class1 collagenase experimental SAS data
DAMMIF model
Sample: Class1 collagenase monomer, 27 kDa Hathewaya histolytica protein
Buffer: 10 mM HEPES 100 mM NaCL, 2% glycerol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Sep 14
Structural characterization of bacterial collagenases University of Arkansas PhD thesis 2431 (2017)
Bauer R
RgGuinier 2.5 nm
Dmax 9.4 nm
VolumePorod 36 nm3

SASDCP2 – Tandem CBD from Clostridium histolyticum ColG collagenase at pCa 6

Class1 collagenase experimental SAS data
DAMMIF model
Sample: Class1 collagenase monomer, 27 kDa Hathewaya histolytica protein
Buffer: 10 mM HEPES 100 mM NaCL, 2% glycerol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 14
Structural characterization of bacterial collagenases University of Arkansas PhD thesis 2431 (2017)
Bauer R
RgGuinier 2.6 nm
Dmax 12.8 nm
VolumePorod 33 nm3

SASDB32 – Human Filamin A Ig-like domains 16-17 truncation (1782-1956)

Human Filamin A Ig-like domains 16-17 experimental SAS data
DAMMIN model
Sample: Human Filamin A Ig-like domains 16-17 monomer, 19 kDa Homo sapiens protein
Buffer: 20 mM Tris 50 mM NaCl 10 mM DTT, pH:
Experiment: SAXS data collected at BM29, ESRF on 2013 Sep 30
Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing. Sci Rep 7(1):4218 (2017)
Seppälä J, Bernardi RC, Haataja TJK, Hellman M, Pentikäinen OT, Schulten K, Permi P, Ylänne J, Pentikäinen U
RgGuinier 1.8 nm
Dmax 6.2 nm
VolumePorod 31 nm3

SASDB42 – Human Filamin A Ig-like domains 16-17* truncation (1782-1956) L1788R patient mutation

Human Filamin A Ig-like domains 16-17* experimental SAS data
DAMMIN model
Sample: Human Filamin A Ig-like domains 16-17* monomer, 19 kDa Homo sapiens protein
Buffer: 20 mM Tris 50 mM NaCl 10 mM DTT, pH:
Experiment: SAXS data collected at BM29, ESRF on 2013 Sep 30
Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing. Sci Rep 7(1):4218 (2017)
Seppälä J, Bernardi RC, Haataja TJK, Hellman M, Pentikäinen OT, Schulten K, Permi P, Ylänne J, Pentikäinen U
RgGuinier 2.4 nm
Dmax 8.3 nm
VolumePorod 37 nm3

SASDBZ8 – Single stranded poly-deoxyadenosine DNA (30mer, dA30) in 100 mM NaCl

Poly-deoxyadenosine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxyadenosine (30mer) monomer, 9 kDa DNA
Buffer: 1mM Na MOPS, 100mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
Plumridge A, Meisburger SP, Andresen K, Pollack L
RgGuinier 2.7 nm
Dmax 10.0 nm
VolumePorod 16 nm3

SASDB29 – Single stranded poly-deoxyadenosine DNA (30mer, dA30) in 200 mM NaCl

Poly-deoxyadenosine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxyadenosine (30mer) monomer, 9 kDa DNA
Buffer: 1mM Na MOPS, 200mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
Plumridge A, Meisburger SP, Andresen K, Pollack L
RgGuinier 2.7 nm
Dmax 9.5 nm
VolumePorod 15 nm3

SASDB39 – Single stranded poly-deoxythymidine DNA (30mer, dT30) in 100 mM NaCl

Poly-deoxythymidine (30mer) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Poly-deoxythymidine (30mer) monomer, 9 kDa DNA
Buffer: 1mM Na MOPS, 100mM NaCl, pH: 7
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Apr 1
The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 45(7):3932-3943 (2017)
Plumridge A, Meisburger SP, Andresen K, Pollack L
RgGuinier 2.8 nm