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SASBDB, a repository for biological small-angle scattering data.

Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI - Nucleic Acids Res. (2014)

Bottom Line: Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically.The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf).At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany.

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Detailed representation of an SASBDB entry (based on http://www.sasbdb.org/data/SASDAU4/). (A) Title of the publication (or project in case of unpublished data). (B) List of authors, main contributor(s) to the SAS results highlighted in bold; journal reference and a link to PubMed if available. (C) SASBDB ID and the tile of the entry. (D) Name of the macromolecule(s) that were measured. (E) Experimental scattering data (logarithmic plot). (F, G) Fit to the experimental data from the respective model(s) displayed on the right. (H) Experimental details, buffer and a brief description of the data reduction steps. (I) Drop-down list of files available for download, including a zip archive with all files related to the entry. (J) Summary of the overall parameters: MW estimated from the forward scattering, molecular weight expected from the sequence and the oligomeric state, Porod volume. (K) Guinier plot with the linear fit and estimated values of the forward scattering I(0) and the radius of gyration Rg. (L) Dimensionless Kratky plot. (M) Distance distribution function p(r) and the maximum particle dimension Dmax. (N) Ab initio model. (O) Hybrid model. On clicking the models switch to the interactive 3D mode. (P) Biological details of each measured macromolecule, sequence and a link to UniProt if available.
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Figure 1: Detailed representation of an SASBDB entry (based on http://www.sasbdb.org/data/SASDAU4/). (A) Title of the publication (or project in case of unpublished data). (B) List of authors, main contributor(s) to the SAS results highlighted in bold; journal reference and a link to PubMed if available. (C) SASBDB ID and the tile of the entry. (D) Name of the macromolecule(s) that were measured. (E) Experimental scattering data (logarithmic plot). (F, G) Fit to the experimental data from the respective model(s) displayed on the right. (H) Experimental details, buffer and a brief description of the data reduction steps. (I) Drop-down list of files available for download, including a zip archive with all files related to the entry. (J) Summary of the overall parameters: MW estimated from the forward scattering, molecular weight expected from the sequence and the oligomeric state, Porod volume. (K) Guinier plot with the linear fit and estimated values of the forward scattering I(0) and the radius of gyration Rg. (L) Dimensionless Kratky plot. (M) Distance distribution function p(r) and the maximum particle dimension Dmax. (N) Ab initio model. (O) Hybrid model. On clicking the models switch to the interactive 3D mode. (P) Biological details of each measured macromolecule, sequence and a link to UniProt if available.

Mentions: Experimental solution scattering data are presented as log10I(s) versus s (Figure 1E) where I(s) is the intensity and s is the modulus of the scattering vector (in nm−1). Due to experimental errors a small number of intensities may be negative, these data points are shown as absolute values in red. To facilitate the comparison of different data plots the following convention is observed: one order of magnitude on the I(s) axis has the same length (in pixels) as one inverse nanometer on the s axis. Plots of experimental data that contain angles higher than 6 nm−1 are displayed with a horizontal scroll bar. This is a convenient way of representing wide-angle X-ray scattering (WAXS) data.


SASBDB, a repository for biological small-angle scattering data.

Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI - Nucleic Acids Res. (2014)

Detailed representation of an SASBDB entry (based on http://www.sasbdb.org/data/SASDAU4/). (A) Title of the publication (or project in case of unpublished data). (B) List of authors, main contributor(s) to the SAS results highlighted in bold; journal reference and a link to PubMed if available. (C) SASBDB ID and the tile of the entry. (D) Name of the macromolecule(s) that were measured. (E) Experimental scattering data (logarithmic plot). (F, G) Fit to the experimental data from the respective model(s) displayed on the right. (H) Experimental details, buffer and a brief description of the data reduction steps. (I) Drop-down list of files available for download, including a zip archive with all files related to the entry. (J) Summary of the overall parameters: MW estimated from the forward scattering, molecular weight expected from the sequence and the oligomeric state, Porod volume. (K) Guinier plot with the linear fit and estimated values of the forward scattering I(0) and the radius of gyration Rg. (L) Dimensionless Kratky plot. (M) Distance distribution function p(r) and the maximum particle dimension Dmax. (N) Ab initio model. (O) Hybrid model. On clicking the models switch to the interactive 3D mode. (P) Biological details of each measured macromolecule, sequence and a link to UniProt if available.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 1: Detailed representation of an SASBDB entry (based on http://www.sasbdb.org/data/SASDAU4/). (A) Title of the publication (or project in case of unpublished data). (B) List of authors, main contributor(s) to the SAS results highlighted in bold; journal reference and a link to PubMed if available. (C) SASBDB ID and the tile of the entry. (D) Name of the macromolecule(s) that were measured. (E) Experimental scattering data (logarithmic plot). (F, G) Fit to the experimental data from the respective model(s) displayed on the right. (H) Experimental details, buffer and a brief description of the data reduction steps. (I) Drop-down list of files available for download, including a zip archive with all files related to the entry. (J) Summary of the overall parameters: MW estimated from the forward scattering, molecular weight expected from the sequence and the oligomeric state, Porod volume. (K) Guinier plot with the linear fit and estimated values of the forward scattering I(0) and the radius of gyration Rg. (L) Dimensionless Kratky plot. (M) Distance distribution function p(r) and the maximum particle dimension Dmax. (N) Ab initio model. (O) Hybrid model. On clicking the models switch to the interactive 3D mode. (P) Biological details of each measured macromolecule, sequence and a link to UniProt if available.
Mentions: Experimental solution scattering data are presented as log10I(s) versus s (Figure 1E) where I(s) is the intensity and s is the modulus of the scattering vector (in nm−1). Due to experimental errors a small number of intensities may be negative, these data points are shown as absolute values in red. To facilitate the comparison of different data plots the following convention is observed: one order of magnitude on the I(s) axis has the same length (in pixels) as one inverse nanometer on the s axis. Plots of experimental data that contain angles higher than 6 nm−1 are displayed with a horizontal scroll bar. This is a convenient way of representing wide-angle X-ray scattering (WAXS) data.

Bottom Line: Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically.The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf).At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany.

Show MeSH
Related in: MedlinePlus