SASDBD6

Single stranded poly-deoxythymidine DNA (30mer, dT30)

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2020-08-28T15:28:04.558399+02:00

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Single stranded poly-deoxythymidine DNA (30mer, dT30)

Concentration	0.45 – 1.8	Buffer / pH	1 mM Na-MOPS, 20 mM NaCl / 7.0
Experimental temperature	—	Facility / beamline	Cornell High Energy Synchrotron Source (CHESS) / G1
Wavelength	0.111 nm	Exposure	10.0 s × 20

Molecular Components

Component	Type / organism	UniProt and Construct	Oligomeric State	Molecular weight
Poly-deoxythymidine (30mer) View sequence TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	DNA—	——–—	monomerMolecule count 1	9.064 kDa

Experimental Curves

Curve	Points / columns	q range	Uncertainty quality	Negative-intensity points	Source file
1	281[3]	0.01–0.29 1/A	Has uncertainty columnMissing 0	0	sasbdb/entries/d6/sasdbd6/source/SASDBD6.dat

▼

2. Measurements Reported by SASBDB Reported Results

Metric	Method	Value	Uncertainty	Unit
dmax	P(r)	10.7	—	Å
i0	Guinier	50.22	0.38	—
mw	Experimental	0.0	—	kDa
rg	Guinier	2.96	0.03	Å
rg	P(r)	3.101	—	Å

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

▼

3. Source Fits and Models Source Fits & Models

Fit 1 · —

χ²: 1.07CorMap p: 0.008Unit: 1/A

Fit data Fit plot Residual plot

Model	Name / Type	Software	Symmetry	Model MW	PDB Declaration	Source file
1	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
2	—dummy	Custom in-house	—	—	—	Model Image
3	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
4	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
5	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
6	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
7	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
8	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
9	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
10	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
11	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
12	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
13	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
14	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
15	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
16	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
17	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
18	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
19	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image
20	—dummy	Custom in-house GAJOE1.3	—	—	—	Model Image

▶

4. Source File Index Source Files

Category	Path	Download status	Size
curve	sasbdb/entries/d6/sasdbd6/source/SASDBD6.dat	downloaded	5933
full_entry_zip	sasbdb/entries/d6/sasdbd6/source/SASDBD6.zip	downloaded	213238
pddf	sasbdb/entries/d6/sasdbd6/source/SASDBD6.out	downloaded	27676
sascif	sasbdb/entries/d6/sasdbd6/source/SASDBD6.sascif	downloaded	1152950
summary	sasbdb/entries/d6/sasdbd6/source/summary.json	downloaded	18306

▶

5. Experiment Description and Publication Experiment & Publication

▼

6. Complete Source Record Complete Source Record

The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer name	1 mM Na-MOPS, 20 mM NaCl	Buffer concentration	—
pH	7.0	Additives	—
Buffer description	—
Purity measurement method	—	Extinction coefficient	—
Absorbance	—	Scattering contrast	—
Specific volume / dry volume	— / —	Mixture / deuteration	— / —

Acquisition Conditions and Instrument

Measurement date	2016-04-01	Storage / measurement temperature	— / —
Exposure time	10.0	Frames	20
Wavelength	0.111	Sample-to-detector distance	1.8
Source	X-ray synchrotron	Detector	Finger Lakes CCD
Facility / beamline	Cornell High Energy Synchrotron Source (CHESS) / G1 · Ithaca, NY, USA
q range	0.1 – 2.9	Sample volume / flow rate	— / —

Original SASBDB Plots

Downloadable Files

Category	File	Status	Size	Checksum	Download and View
curve	sasbdb/entries/d6/sasdbd6/source/SASDBD6.dat	downloaded	5933	dab5ae093fd57a368d4dc01f7e9f483c388e601397656a873ac0297ac95b3d03	DownloadView source fileSource site
full_entry_zip	sasbdb/entries/d6/sasdbd6/source/SASDBD6.zip	downloaded	213238	3aa3702667b58c868572e52aa8e797edf1cb21e741feb3b19c7c15cc6b91794b	DownloadView source fileSource site
pddf	sasbdb/entries/d6/sasdbd6/source/SASDBD6.out	downloaded	27676	61afae4611d6f65f6d3d8c9b16416f013c2838ad5a035fd2eb6f6902dbd1151d	DownloadView source fileSource site
sascif	sasbdb/entries/d6/sasdbd6/source/SASDBD6.sascif	downloaded	1152950	219d005cf69a389c30e7af49e335d67df0f366562ed6370058a4ba1da0d54120	DownloadView source fileSource site
summary	sasbdb/entries/d6/sasdbd6/source/summary.json	downloaded	18306	8d240a5dada40a08da476fd5a886245c51758082d9ffec786824c272f40658ab	DownloadView source fileSource site

curve：source record

{
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  "role": "curve",
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  "size": 5933,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/intensities_files/SASDBD6.dat"
}

full_entry_zip：source record and ZIP contents (24 items)

{
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  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/zip_directories/SASDBD6.zip",
  "zip_member_count": 24,
  "zip_members": [
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    {
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    },
    {
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      "size": 47163
    },
    {
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      "name": "SASDBD6/SASDBD6_fit1_model15.pdb",
      "size": 47163
    },
    {
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      "size": 47163
    },
    {
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      "name": "SASDBD6/SASDBD6_fit1_model17.pdb",
      "size": 47163
    },
    {
      "crc32": "87c19bd3",
      "name": "SASDBD6/SASDBD6_fit1_model18.pdb",
      "size": 47163
    },
    {
      "crc32": "6f429481",
      "name": "SASDBD6/SASDBD6_fit1_model19.pdb",
      "size": 47163
    },
    {
      "crc32": "7604a43b",
      "name": "SASDBD6/SASDBD6_fit1_model20.pdb",
      "size": 47163
    },
    {
      "crc32": "5db0107c",
      "name": "SASDBD6/SASDBD6_fit1_rg_distribution.txt",
      "size": 448
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  ],
  "zip_validation": "central_directory_readable"
}

pddf：source record

{
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  "role": "pddf",
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  "size": 27676,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/p_of_R_files/SASDBD6.out"
}

sascif：source record

{
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  "role": "sascif",
  "sha256": "219d005cf69a389c30e7af49e335d67df0f366562ed6370058a4ba1da0d54120",
  "size": 1152950,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBD6.sascif"
}

summary：source record

{
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  "size": 18306,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDBD6/"
}

All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json：403 field values

Field path	Raw value
code	SASDBD6
status	Published
type_of_curve	Extrapolated to infinite dilution
angular_unit	1/A
project.title	Visualizing single-stranded nucleic acids in solution.
project.publication.title	Visualizing single-stranded nucleic acids in solution.
project.publication.author_list	Plumridge A, Meisburger SP, Pollack L
project.publication.journal	Nucleic Acids Res
project.publication.doi	10.1093/nar/gkw1297
project.publication.pmid	28034955
project.publication.published_date	2017 May 19
project.status	released
project.submitted_date	2016-09-06
project.released_date	2017-01-28
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDBD6.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDBD6.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBD6_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBD6_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBD6_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBD6_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDBD6.sascif
experiment.instrument.detector.type	CCD
experiment.instrument.detector.name	Finger Lakes CCD
experiment.instrument.detector.resolution	0.0
experiment.instrument.name	Cornell High Energy Synchrotron Source (CHESS)
experiment.instrument.city	Ithaca, NY
experiment.instrument.country	USA
experiment.instrument.beamline_name	G1
experiment.instrument.beam_geometry
experiment.instrument.type_of_source	X-ray synchrotron
experiment.instrument.point_source	null
experiment.instrument.line_collimation	null
experiment.instrument.sample_path_length	null
experiment.instrument.line_collimation_slitlength	null
experiment.instrument.line_collimation_integrationwidth	null
experiment.instrument.xray_energy	null
experiment.instrument.beam_profile_ah	null
experiment.instrument.beam_profile_al	null
experiment.sample.molecule[0].long_name	Poly-deoxythymidine (30mer)
experiment.sample.molecule[0].short_name	dT30
experiment.sample.molecule[0].sequence	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
experiment.sample.molecule[0].organism	null
experiment.sample.molecule[0].uniprot_code	null
experiment.sample.molecule[0].uniprot_range_first	null
experiment.sample.molecule[0].uniprot_range_last	null
experiment.sample.molecule[0].oligomerization	monomer
experiment.sample.molecule[0].molecular_type	DNA
experiment.sample.molecule[0].uniprot_sequence	null
experiment.sample.molecule[0].mw	9.064
experiment.sample.molecule[0].total_mw	9.064
experiment.sample.molecule[0].number_molecules	1
experiment.sample.molecule[0].complex_state	False
experiment.sample.molecule[0].deuteration	null
experiment.sample.molecule[0].molecule_source	biological
experiment.sample.molecule[0].molecule_description	null
experiment.sample.buffer.name	1 mM Na-MOPS, 20 mM NaCl
experiment.sample.buffer.concentration_unit	null
experiment.sample.buffer.comment	null
experiment.sample.buffer.additive	null
experiment.sample.buffer.concentration	null
experiment.sample.buffer.pka	null
experiment.sample.buffer.ph	7.0
experiment.sample.buffer.deuteration	null
experiment.sample.purity_method	null
experiment.sample.name	Single stranded poly-deoxythymidine DNA (30mer, dT30)
experiment.sample.ext_coefficient	null
experiment.sample.contrast	null
experiment.sample.specific_vol	null
experiment.sample.dry_vol	null
experiment.sample.absorbption	null
experiment.sample.deuteration	null
experiment.sample.mixture	null
experiment.contributor[0].affiliation[0].short_name	null
experiment.contributor[0].affiliation[0].address	Ithaca, NY, United States
experiment.contributor[0].affiliation[0].full_name	Cornell University
experiment.contributor[0].affiliation[0].webpage	https://www.cornell.edu/
experiment.contributor[0].contributor_name	Alex
experiment.contributor[0].contributor_surname	Plumridge
experiment.contributor[0].orcid	null
experiment.concentration_method	null
experiment.concentration_unit	null
experiment.date	2016-04-01
experiment.storage_temperature	null
experiment.cell_temperature	null
experiment.exposure_time	10.0
experiment.number_of_frames	20
experiment.wavelength	0.111
experiment.sample_detector_distance	1.8
experiment.concentration_min	0.45
experiment.concentration_max	1.8
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.1
experiment.s_max	2.9
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model1_img.png
fits[0].models[0].software	Custom in-house
fits[0].models[0].pdb_link	[]
fits[0].models[0].model_title	null
fits[0].models[0].type_of_model	dummy
fits[0].models[0].software_version	GAJOE1.3
fits[0].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model1.pdb
fits[0].models[0].model_mw	null
fits[0].models[0].bead_radius	1.9
fits[0].models[0].log	null
fits[0].models[0].symmetry
fits[0].models[0].comment	Custom SAXS model building/fitting method - state 1
fits[0].models[0].user	156
fits[0].models[1].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model2_img.png
fits[0].models[1].software	Custom in-house
fits[0].models[1].pdb_link	[]
fits[0].models[1].model_title	null
fits[0].models[1].type_of_model	dummy
fits[0].models[1].software_version
fits[0].models[1].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model2.pdb
fits[0].models[1].model_mw	null
fits[0].models[1].bead_radius	1.9
fits[0].models[1].log	null
fits[0].models[1].symmetry
fits[0].models[1].comment	Custom SAXS model building/fitting method - state 2
fits[0].models[1].user	156
fits[0].models[2].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model3_img.png
fits[0].models[2].software	Custom in-house
fits[0].models[2].pdb_link	[]
fits[0].models[2].model_title	null
fits[0].models[2].type_of_model	dummy
fits[0].models[2].software_version	GAJOE1.3
fits[0].models[2].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model3.pdb
fits[0].models[2].model_mw	null
fits[0].models[2].bead_radius	1.9
fits[0].models[2].log	null
fits[0].models[2].symmetry
fits[0].models[2].comment	Custom SAXS model building/fitting method - state 3
fits[0].models[2].user	156
fits[0].models[3].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model4_img.png
fits[0].models[3].software	Custom in-house
fits[0].models[3].pdb_link	[]
fits[0].models[3].model_title	null
fits[0].models[3].type_of_model	dummy
fits[0].models[3].software_version	GAJOE1.3
fits[0].models[3].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model4.pdb
fits[0].models[3].model_mw	null
fits[0].models[3].bead_radius	1.9
fits[0].models[3].log	null
fits[0].models[3].symmetry
fits[0].models[3].comment	Custom SAXS model building/fitting method - state 4
fits[0].models[3].user	156
fits[0].models[4].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model5_img.png
fits[0].models[4].software	Custom in-house
fits[0].models[4].pdb_link	[]
fits[0].models[4].model_title	null
fits[0].models[4].type_of_model	dummy
fits[0].models[4].software_version	GAJOE1.3
fits[0].models[4].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model5.pdb
fits[0].models[4].model_mw	null
fits[0].models[4].bead_radius	1.9
fits[0].models[4].log	null
fits[0].models[4].symmetry
fits[0].models[4].comment	Custom SAXS model building/fitting method - state 5
fits[0].models[4].user	156
fits[0].models[5].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model6_img.png
fits[0].models[5].software	Custom in-house
fits[0].models[5].pdb_link	[]
fits[0].models[5].model_title	null
fits[0].models[5].type_of_model	dummy
fits[0].models[5].software_version	GAJOE1.3
fits[0].models[5].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model6.pdb
fits[0].models[5].model_mw	null
fits[0].models[5].bead_radius	1.9
fits[0].models[5].log	null
fits[0].models[5].symmetry
fits[0].models[5].comment	Custom SAXS model building/fitting method - state 6
fits[0].models[5].user	156
fits[0].models[6].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model7_img.png
fits[0].models[6].software	Custom in-house
fits[0].models[6].pdb_link	[]
fits[0].models[6].model_title	null
fits[0].models[6].type_of_model	dummy
fits[0].models[6].software_version	GAJOE1.3
fits[0].models[6].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model7.pdb
fits[0].models[6].model_mw	null
fits[0].models[6].bead_radius	1.9
fits[0].models[6].log	null
fits[0].models[6].symmetry
fits[0].models[6].comment	Custom SAXS model building/fitting method - state 7
fits[0].models[6].user	156
fits[0].models[7].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDBD6_fit1_model8_img.png
fits[0].models[7].software	Custom in-house
fits[0].models[7].pdb_link	[]
fits[0].models[7].model_title	null
fits[0].models[7].type_of_model	dummy
fits[0].models[7].software_version	GAJOE1.3
fits[0].models[7].model_data	https://www.sasbdb.org/media/pdb_file/SASDBD6_fit1_model8.pdb
fits[0].models[7].model_mw	null
fits[0].models[7].bead_radius	1.9
fits[0].models[7].log	null
fits[0].models[7].symmetry
fits[0].models[7].comment	Custom SAXS model building/fitting method - state 8
fits[0].models[7].user	156
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i0_calibration_standard	null
description	null
experiment_description	Synchrotron SAXS data from solutions of single stranded poly-deoxythymidine DNA (30mer, dT30) in 1mM Na MOPS, 20mM NaCl, pH 7 were collected on the G1 Beamline camera on the storage ring CHESS (Ithaca, USA) using a CCD Finger Lakes CCD detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 1.8 mg/ml were measured . 20 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for sample concentration. The low angle data collected at lower concentrations were merged with the higher concentration data to yield the final composite scattering curve.
tags	[]
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i0_calibration_standard_data	null
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symmetry	null
last_modified	2020-08-28T15:28:04.558399+02:00
bragg_peak	[]

manifest.json：36 field values

Field path	Raw value
code	SASDBD6
status	success
started_at	2026-08-11T15:06:44.977543+00:00
finished_at	2026-08-11T15:06:54.738672+00:00
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View the complete summary.json source

{
  "code": "SASDBD6",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/A",
  "project": {
    "title": "Visualizing single-stranded nucleic acids in solution.",
    "publication": {
      "title": "Visualizing single-stranded nucleic acids in solution.",
      "author_list": "Plumridge A, Meisburger SP, Pollack L",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkw1297",
      "pmid": "28034955",
      "published_date": "2017 May 19"
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    "released_date": "2017-01-28"
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      "name": "Cornell High Energy Synchrotron Source (CHESS)",
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      "country": "USA",
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      "type_of_source": "X-ray synchrotron",
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            "short_name": null,
            "address": "Ithaca, NY, United States",
            "full_name": "Cornell University",
            "webpage": "https://www.cornell.edu/"
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View the complete manifest.json source

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Title	Visualizing single-stranded nucleic acids in solution.
Authors	Plumridge A, Meisburger SP, Pollack L
DOI / PMID	10.1093/nar/gkw1297 / 28034955