Browse by MODEL: Ab initio only

SASDHP3 – Optimized Parallel DNA

Optimized Parallel experimental SAS data
DAMFILT model
Sample: Optimized Parallel monomer, 18 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Nov 3
The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res (2020)
Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo TM, Chakravarthy S, Chaires JB, Trent JO
RgGuinier 1.7 nm
Dmax 5.0 nm
VolumePorod 17 nm3

SASDHQ3 – Human Telomerase Reverse Transcriptase Core Promoter (hTERT) PQS2-PQS3 region, WT_PQS23

hTERT core promoter PQS2-PQS3 region experimental SAS data
DAMFILT model
Sample: HTERT core promoter PQS2-PQS3 region monomer, 14 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Nov 3
The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res (2020)
Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo TM, Chakravarthy S, Chaires JB, Trent JO
RgGuinier 1.7 nm
Dmax 5.4 nm
VolumePorod 18 nm3

SASDHR3 – Antiparallel Hairpin PQS2-PQS3 segment DNA, AH_PQS23

Antiparallel Hairpin PQS2-PQS3 segment experimental SAS data
DAMFILT model
Sample: Antiparallel Hairpin PQS2-PQS3 segment monomer, 14 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Nov 3
The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res (2020)
Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo TM, Chakravarthy S, Chaires JB, Trent JO
RgGuinier 2.0 nm
Dmax 6.4 nm
VolumePorod 18 nm3

SASDMJ4 – Lysozyme amyloid fibril (LAF)

lysozyme amyloid fibril experimental SAS data
DAMMIF model
Sample: Lysozyme amyloid fibril, 14 kDa Gallus gallus protein
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 5
Effect of the concentration of protein and nanoparticles on the structure of biohybrid nanocomposites. Biopolymers 111(2):e23342 (2020)
Majorošová J, Schroer MA, Tomašovičová N, Batková M, Hu PS, Kubovčíková M, Svergun DI, Kopčanský P
RgGuinier 30.2 nm
Dmax 120.0 nm

SASDML4 – LAF + MNP (r = 5.6 nm) nanocomposite

lysozyme amyloid fibrilFe3O4 nanoparticles; radius 5.6 nm (AFM based) experimental SAS data
DAMMIF model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; radius 5.6 nm (AFM based) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 8
Effect of the concentration of protein and nanoparticles on the structure of biohybrid nanocomposites. Biopolymers 111(2):e23342 (2020)
Majorošová J, Schroer MA, Tomašovičová N, Batková M, Hu PS, Kubovčíková M, Svergun DI, Kopčanský P
RgGuinier 29.4 nm
Dmax 80.0 nm

SASDH24 – Calcium-Activated Chloride Channel Regulator 1 VWA domain

Calcium-activated chloride channel regulator 1 experimental SAS data
DAMFILT model
Sample: Calcium-activated chloride channel regulator 1 monomer, 20 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 150 mM NaCl, 2% glycerol, pH: 7.4
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Jun 6
Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement. Cell Rep 30(4):1141-1151.e3 (2020)
Berry KN, Brett TJ
RgGuinier 1.8 nm
Dmax 6.6 nm

SASDH34 – Calcium-Activated Chloride Channel Regulator 1 CAT-CYS-VWA domain construct

Calcium-activated chloride channel regulator 1 experimental SAS data
DAMFILT model
Sample: Calcium-activated chloride channel regulator 1 monomer, 52 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 150 mM NaCl, 2% glycerol, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2017 Jun 6
Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement. Cell Rep 30(4):1141-1151.e3 (2020)
Berry KN, Brett TJ
RgGuinier 3.4 nm
Dmax 13.4 nm

SASDH93 – Braveheart Fragment 1

Braveheart Fragment 1 experimental SAS data
DAMMIN model
Sample: Braveheart Fragment 1 monomer, 116 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
Kim D, Thiel B, Mrozowich T, Hennelly S, Hofacker I, Patel T, Sanbonmatsu K
RgGuinier 8.4 nm
Dmax 24.0 nm
VolumePorod 426 nm3

SASDHA3 – Braveheart Fragment 2

Braveheart Fragment 2 experimental SAS data
DAMMIN model
Sample: Braveheart Fragment 2 monomer, 112 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
Kim D, Thiel B, Mrozowich T, Hennelly S, Hofacker I, Patel T, Sanbonmatsu K
RgGuinier 8.1 nm
Dmax 27.2 nm
VolumePorod 443 nm3

SASDHB3 – Braveheart Fragment 3

Braveheart Fragment 3 experimental SAS data
DAMMIN model
Sample: Braveheart Fragment 3 monomer, 111 kDa Homo sapiens RNA
Buffer: 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH: 7.6
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jun 23
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Nature Communications 11(1) (2020)
Kim D, Thiel B, Mrozowich T, Hennelly S, Hofacker I, Patel T, Sanbonmatsu K
RgGuinier 6.5 nm
Dmax 20.5 nm
VolumePorod 492 nm3