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22 hits found for Bierma

SASDPP4 – Consensus SAXS Profile - Ribonuclease A

Ribonuclease pancreatic experimental SAS data
DAMMIN model
Sample: Ribonuclease pancreatic monomer, 14 kDa Bos taurus protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.5 nm
Dmax 4.9 nm
VolumePorod 18 nm3

SASDPQ4 – Consensus SAXS Profile - Urate Oxidase

Uricase experimental SAS data
DAMMIN model
Sample: Uricase tetramer, 136 kDa Aspergillus flavus protein
Buffer: 100 mM Tris, 150 mM NaCl, pH: 8
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 3.2 nm
Dmax 9.2 nm
VolumePorod 220 nm3

SASDPR4 – Consensus SAXS Profile - Xylose Isomerase

Xylose isomerase experimental SAS data
DAMMIN model
Sample: Xylose isomerase tetramer, 173 kDa Streptomyces rubiginosus protein
Buffer: ConsensusBuffer_50 mM Tris, 100 mM NaCl, 1 mM MgCl2, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 3.3 nm
Dmax 10.1 nm
VolumePorod 243 nm3

SASDPS4 – Consensus SAXS Profile - Xylanase

Endo-1,4-beta-xylanase experimental SAS data
DAMMIN model
Sample: Endo-1,4-beta-xylanase monomer, 21 kDa Trichoderma longibrachiatum protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.6 nm
Dmax 5.1 nm
VolumePorod 27 nm3

SASDPT4 – Consensus SAXS Profile - Lysozyme

Lysozyme C experimental SAS data
DAMMIN model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 50 mM sodium citrate, 150 mM NaCl, pH: 4.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.5 nm
Dmax 4.8 nm
VolumePorod 19 nm3

SASDPU4 – Consensus SANS Profile - Ribonuclease A in 100% v/v D2O buffer

Ribonuclease pancreatic experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Ribonuclease pancreatic monomer, 14 kDa Bos taurus protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.4 nm
Dmax 4.4 nm

SASDPV4 – Consensus SANS Profile - Lysozyme in 100% v/v D2O buffer

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 50 mM sodium citrate, 150 mM NaCl, pH: 4.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.2 nm
Dmax 3.8 nm

SASDPW4 – Consensus SANS Profile - Xylanase in 100% v/v D2O buffer

Endo-1,4-beta-xylanase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Endo-1,4-beta-xylanase monomer, 21 kDa Trichoderma longibrachiatum protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.5 nm
Dmax 4.4 nm

SASDPX4 – Consensus SANS Profile - Urate oxidase in 100% v/v D2O buffer

Uricase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Uricase tetramer, 136 kDa Aspergillus flavus protein
Buffer: 100 mM Tris, 150 mM NaCl, pH: 8
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 3.1 nm
Dmax 9.3 nm

SASDPY4 – Consensus SANS Profile - Xylose isomerase in 100% v/v D2O buffer

Xylose isomerase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Xylose isomerase tetramer, 173 kDa Streptomyces rubiginosus protein
Buffer: 50 mM Tris, 100 mM NaCl, 1 mM MgCl2, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 6
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 3.1 nm
Dmax 9.5 nm

SASDPZ4 – Consensus SANS Profile - Lysozyme in H2O buffer

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 50 mM sodium citrate, 150 mM NaCl, pH: 4.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 22
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.4 nm
Dmax 4.8 nm

SASDP25 – Consensus SANS Profile - Ribonuclease A in H2O buffer

Ribonuclease pancreatic experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Ribonuclease pancreatic monomer, 14 kDa Bos taurus protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 22
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.5 nm
Dmax 4.1 nm

SASDP35 – Consensus SANS Profile - Xylanase in H2O buffer

Endo-1,4-beta-xylanase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Endo-1,4-beta-xylanase monomer, 21 kDa Trichoderma longibrachiatum protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 22
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 1.6 nm
Dmax 4.3 nm

SASDP45 – Consensus SANS Profile - Urate oxidase in H2O buffer

Uricase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Uricase tetramer, 136 kDa Aspergillus flavus protein
Buffer: 100 mM Tris, 150 mM NaCl, pH: 8
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 24
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 3.2 nm
Dmax 9.1 nm

SASDP55 – Consensus SANS Profile - Xylose isomerase in H2O buffer

Xylose isomerase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Xylose isomerase tetramer, 173 kDa Streptomyces rubiginosus protein
Buffer: 50 mM Tris, 100 mM NaCl, 1 mM MgCl2, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 24
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
...Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q...
RgGuinier 3.3 nm
Dmax 9.7 nm

SASDJV4 – X-ray repair cross-complementing proteins 5ΔCTR and 6

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5 ΔCTR experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 ΔCTR monomer, 64 kDa Homo sapiens protein
Buffer: 50 mM Hepes, 50 mM KCl, 5 mM MgCl2, 5% glycerol and 0.2 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 12
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 3.8 nm
Dmax 12.5 nm
VolumePorod 240 nm3

SASDJU4 – X-ray repair cross-complementing proteins 5 and 6

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5 experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
Buffer: 50 mM Hepes, 50 mM KCl, 5 mM MgCl2, 5% glycerol and 0.2 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 12
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 4.2 nm
Dmax 14.9 nm
VolumePorod 253 nm3

SASDJW4 – X-ray repair cross-complementing proteins 5 and 6-DNA

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5Y-DNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
Y-DNA monomer, 18 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2010 Jan 8
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 4.1 nm
Dmax 14.8 nm
VolumePorod 280 nm3

SASDJX4 – DNA-dependent protein kinase catalytic subunit (DNA-PKcs)

DNA-dependent protein kinase catalytic subunit experimental SAS data
BILBOMD model
Sample: DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 5.6 nm
Dmax 15.6 nm
VolumePorod 1040 nm3

SASDJY4 – Autophosphorylated DNA-dependent protein kinase (DNA-PKcs)

DNA-dependent protein kinase catalytic subunit experimental SAS data
BILBOMD model
Sample: DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
Buffer: 50 mM Tris-HCl, 100 mM KCl, 5% (v/v) glycerol, 0.2 mM EDTA containing 0.1 mM benzamidine, 0.2 mM PMSF and 0.2 µg/ml pepstatin, pH: 8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2010 Jan 8
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 5.5 nm
Dmax 16.1 nm
VolumePorod 918 nm3

SASDJZ4 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer )

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5DNA-dependent protein kinase catalytic subunitdsDNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
dsDNA dimer, 21 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 6.5 nm
Dmax 23.1 nm
VolumePorod 1090 nm3

SASDJ25 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer/dimer)

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5DNA-dependent protein kinase catalytic subunitdsDNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
dsDNA dimer, 21 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
...Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 7.5 nm
Dmax 29.4 nm
VolumePorod 1440 nm3