Browse by MODEL: Ab initio only

SASDM99 – Lysozyme crystallization solutions with precipitants from crystallization kits CS 1 and CS2 (mixture of monomers, dimers and octamers, with octamer volume fractions from 4.9% to 21.1%)

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 200 mM K/Na tartrate, 100 mM tri-sodium citrate pH 5.6, 2.0 M ammonium sulfate, pH: 5.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Aug 28
The Relationship of Precursor Cluster Concentration in a Saturated Crystallization Solution to Long-Range Order During the Transition to the Solid Phase. Acta Naturae 15(1):58-68 (2023)
Marchenkova MA, Boikova AS, Ilina KB, Konarev PV, Pisarevsky YV, Dyakova YA, Kovalchuk MV
RgGuinier 2.4 nm

SASDWA7 – Dihydroneopterin aldolase from H.pylori (HpDHNA:Pterin)

Dihydroneopterin aldolase experimental SAS data
DAMMIN model
Sample: Dihydroneopterin aldolase tetramer, 55 kDa Helicobacter pylori (strain … protein
Buffer: 25 mM Tris-HCl pH 7.5 and 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Apr 5
Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design. Curr Res Struct Biol 5:100095 (2023)
Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X
RgGuinier 2.5 nm
Dmax 7.3 nm
VolumePorod 77 nm3

SASDPW2 – mTIP60-Ba (metal-ion induced 60-mer complex of TIP60 (K67E) mutant with barium ions)

TIP60 (K67E) mutant (metal-ion induced 60-mer complex with barium ions)Barium ion experimental SAS data
DAMMIN model
Sample: TIP60 (K67E) mutant (metal-ion induced 60-mer complex with barium ions), 1066 kDa Artificial protein protein
Barium ion 0, 8 kDa
Buffer: 25 mM HEPES, 100 mM NaCl, 5% glycerol, 5 mM BaCl2, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2021 May 23
Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc (2022)
Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K
RgGuinier 9.6 nm
Dmax 21.8 nm

SASDPX2 – TIP60 (K67E) mutant (dimer) with EDTA

TIP60 (K67E) mutant with EDTA experimental SAS data
DAMMIN model
Sample: TIP60 (K67E) mutant with EDTA dimer, 36 kDa Artificial protein protein
Buffer: 25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2021 May 23
Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc (2022)
Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K
RgGuinier 3.7 nm
Dmax 12.0 nm

SASDPY2 – SARS-CoV-2 non-structural protein 7-8 (nsp7-8) polyprotein monomer

Replicase polyprotein 1ab experimental SAS data
DAMMIF model
Sample: Replicase polyprotein 1ab monomer, 31 kDa Severe acute respiratory … protein
Buffer: 50 mM Tris, 500 mM NaCl, 5% glycerol, and 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Oct 15
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 2.5 nm
Dmax 8.8 nm
VolumePorod 50 nm3

SASDP23 – SARS-CoV-2 non-structural protein 7-11 (nsp7-11) polyprotein monomer

Replicase polyprotein 1a experimental SAS data
DAMMIF model
Sample: Replicase polyprotein 1a monomer, 60 kDa Severe acute respiratory … protein
Buffer: 20 mM HEPES, 10% glycerol, 500 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Nov 14
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 3.5 nm
Dmax 15.6 nm
VolumePorod 102 nm3

SASDMG9 – Multidrug resistance operon repressor (MexR) of the MexAB-OprM multidrug efflux pump operon of Pseudomonas aeruginosa

Multidrug resistance operon repressor experimental SAS data
DAMFILT model
Sample: Multidrug resistance operon repressor dimer, 32 kDa Pseudomonas aeruginosa protein
Buffer: 20mM HEPES, 150mM NaCl, 10mM DTT, 1% v/v glycerol, pH: 7.1
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Nov 23
Small-angle X-ray and neutron scattering of MexR and its complex with DNA supports a conformational selection binding model Biophysical Journal (2022)
Caporaletti F, Pietras Z, Morad V, Mårtensson L, Gabel F, Wallner B, Martel A, Sunnerhagen M
RgGuinier 2.3 nm
Dmax 7.7 nm
VolumePorod 56 nm3

SASDQ48 – Minimal proline dehydrogenase domain of proline utilization A (SmPutADeltaAlpha2) 1.1 mg/mL

Minimal proline dehydrogenase domain of proline utilization A (design #2) experimental SAS data
OTHER model
Sample: Minimal proline dehydrogenase domain of proline utilization A (design #2) dimer, 87 kDa Sinorhizobium meliloti protein
Buffer: 25 mM HEPES pH 7.6, 150 mM NaCl, and 1mM TCEP, pH: 7.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2022 Apr 12
Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel (2022)
Bogner AN, Ji J, Tanner JJ
RgGuinier 2.7 nm
Dmax 9.5 nm
VolumePorod 102 nm3

SASDQ58 – Minimal proline dehydrogenase domain of proline utilization A (SmPutADeltaAlpha2) 2.3 mg/mL

Minimal proline dehydrogenase domain of proline utilization A (design #2) experimental SAS data
OTHER model
Sample: Minimal proline dehydrogenase domain of proline utilization A (design #2) dimer, 87 kDa Sinorhizobium meliloti protein
Buffer: 25 mM HEPES pH 7.6, 150 mM NaCl, and 1mM TCEP, pH: 7.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2022 Apr 12
Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel (2022)
Bogner AN, Ji J, Tanner JJ
RgGuinier 2.9 nm
Dmax 9.7 nm
VolumePorod 102 nm3

SASDQ68 – Minimal proline dehydrogenase domain of proline utilization A (SmPutADeltaAlpha2) 3.4 mg/mL

Minimal proline dehydrogenase domain of proline utilization A (design #2) experimental SAS data
OTHER model
Sample: Minimal proline dehydrogenase domain of proline utilization A (design #2) dimer, 87 kDa Sinorhizobium meliloti protein
Buffer: 25 mM HEPES pH 7.6, 150 mM NaCl, and 1mM TCEP, pH: 7.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2022 Apr 12
Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel (2022)
Bogner AN, Ji J, Tanner JJ
RgGuinier 3.0 nm
Dmax 9.8 nm
VolumePorod 108 nm3