SASDFJ9

Poly-uridine rU30 in 20 mM NaCl

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2019-12-11T18:17:14.164307+01:00

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Poly-uridine rU30 in 20 mM NaCl

Concentration	0.4 – 1.2	Buffer / pH	1 mM Na-MOPS, 20 mM NaCl, 20 µM EDTA / 7.0
Experimental temperature	25.0	Facility / beamline	Cornell High Energy Synchrotron Source (CHESS) / G1
Wavelength	0.11 nm	Exposure	10.0 s × 30

Molecular Components

Component	Type / organism	UniProt and Construct	Oligomeric State	Molecular weight
Poly-uridine View sequence UUUUUUUUUUUUUUUUUUUUUUUUUUUUUU	RNA—	——–—	monomerMolecule count 1	9.203 kDa

Experimental Curves

Curve	Points / columns	q range	Uncertainty quality	Negative-intensity points	Source file
1	261[3]	0.01–0.27 1/A	Has uncertainty columnMissing 0	0	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.dat

▼

2. Measurements Reported by SASBDB Reported Results

Metric	Method	Value	Uncertainty	Unit
dmax	P(r)	12.0	—	Å
i0	Guinier	29.5	0.48	—
i0	P(r)	29.35	—	—
mw	Experimental	14.0	—	kDa
porod_volume	Porod	29.0	—	Å³
rg	Guinier	3.03	0.08	Å
rg	P(r)	3.11	—	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 · EOM/GAJOE

χ²: 0.958441CorMap p: 0.394932Unit: 1/A

Fit data Fit plot Residual plot

Model	Name / Type	Software	Symmetry	Model MW	PDB Declaration	Source file
1	—atomic	Custom in-house	—	8.789	—	Model Image
2	—atomic	Custom in-house	—	8.789	—	Model Image
3	—atomic	Custom in-house	—	8.789	—	Model Image
4	—atomic	Custom in-house	—	8.789	—	Model Image
5	—atomic	Custom in-house	—	8.789	—	Model Image
6	—atomic	Custom in-house	—	8.789	—	Model Image
7	—atomic	Custom in-house	—	8.789	—	Model Image
8	—atomic	Custom in-house	—	8.789	—	Model Image
9	—atomic	Custom in-house	—	8.789	—	Model Image
10	—atomic	Custom in-house	—	8.789	—	Model Image
11	—atomic	Custom in-house	—	8.789	—	Model Image
12	—atomic	Custom in-house	—	8.789	—	Model Image
13	—atomic	Custom in-house	—	8.789	—	Model Image
14	—atomic	Custom in-house	—	8.789	—	Model Image
15	—atomic	Custom in-house	—	8.789	—	Model Image
16	—atomic	Custom in-house	—	8.789	—	Model Image
17	—atomic	Custom in-house	—	8.789	—	Model Image
18	—atomic	Custom in-house	—	8.789	—	Model Image
19	—atomic	Custom in-house	—	8.789	—	Model Image
20	—atomic	Custom in-house	—	8.789	—	Model Image

▶

4. Source File Index Source Files

Category	Path	Download status	Size
curve	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.dat	downloaded	5502
full_entry_zip	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.zip	downloaded	209461
pddf	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.out	downloaded	21626
sascif	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.sascif	downloaded	1172768
summary	sasbdb/entries/j9/sasdfj9/source/summary.json	downloaded	17348

▶

5. Experiment Description and Publication Experiment & Publication

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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, 20 µM EDTA	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	2015-10-25	Storage / measurement temperature	4.0 / 25.0
Exposure time	10.0	Frames	30
Wavelength	0.11	Sample-to-detector distance	2.04
Source	X-ray synchrotron	Detector	Finger Lakes CCD
Facility / beamline	Cornell High Energy Synchrotron Source (CHESS) / G1 · Ithaca, NY, USA
q range	0.1 – 2.7	Sample volume / flow rate	— / —

Original SASBDB Plots

Downloadable Files

Category	File	Status	Size	Checksum	Download and View
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full_entry_zip	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.zip	downloaded	209461	604012884a45e6e46890fd4a5e1df9df9c6c51b5be32a023a206069cd98a3f7f	DownloadView source fileSource site
pddf	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.out	downloaded	21626	c2d41762af699d0a0881a9d874420603c05f97dc3505288d8c27354ea3b096d2	DownloadView source fileSource site
sascif	sasbdb/entries/j9/sasdfj9/source/SASDFJ9.sascif	downloaded	1172768	661560e6a6ba5e8a2cb999f7cebad6f02a241415234f6d5e8f9d13f731d090a6	DownloadView source fileSource site
summary	sasbdb/entries/j9/sasdfj9/source/summary.json	downloaded	17348	c26647087c67c688797cfb539636d8503ab063b8ebdfe4f19b2d6997ad92e7a4	DownloadView source fileSource site

curve：source record

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full_entry_zip：source record and ZIP contents (23 items)

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pddf：source record

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sascif：source record

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summary：source record

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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	SASDFJ9
status	Published
type_of_curve	Extrapolated to infinite dilution
angular_unit	1/A
project.title	Visualizing disordered single-stranded RNA: connecting sequence, structure and electrostatics.
project.publication.title	Visualizing disordered single-stranded RNA: connecting sequence, structure and electrostatics.
project.publication.author_list	Plumridge A, Andresen K, Pollack L
project.publication.journal	J Am Chem Soc
project.publication.doi	10.1021/jacs.9b04461
project.publication.pmid	31804813
project.publication.published_date	2019 Dec 5
project.status	released
project.submitted_date	2019-07-09
project.released_date	2019-12-11
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDFJ9.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDFJ9.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFJ9_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFJ9_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFJ9_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFJ9_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDFJ9.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-uridine
experiment.sample.molecule[0].short_name	rU30
experiment.sample.molecule[0].sequence	UUUUUUUUUUUUUUUUUUUUUUUUUUUUUU
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	RNA
experiment.sample.molecule[0].uniprot_sequence	null
experiment.sample.molecule[0].mw	9.203
experiment.sample.molecule[0].total_mw	9.203
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, 20 µM EDTA
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	Poly-uridine rU30 in 20 mM NaCl
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	2015-10-25
experiment.storage_temperature	4.0
experiment.cell_temperature	25.0
experiment.exposure_time	10.0
experiment.number_of_frames	30
experiment.wavelength	0.11
experiment.sample_detector_distance	2.04
experiment.concentration_min	0.4
experiment.concentration_max	1.2
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.1
experiment.s_max	2.7
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[0].software_version	null
fits[0].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model1.pdb
fits[0].models[0].model_mw	8.789
fits[0].models[0].bead_radius	null
fits[0].models[0].log	null
fits[0].models[0].symmetry	null
fits[0].models[0].comment	null
fits[0].models[0].user	156
fits[0].models[1].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[1].software_version	null
fits[0].models[1].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model2.pdb
fits[0].models[1].model_mw	8.789
fits[0].models[1].bead_radius	null
fits[0].models[1].log	null
fits[0].models[1].symmetry	null
fits[0].models[1].comment	null
fits[0].models[1].user	156
fits[0].models[2].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[2].software_version	null
fits[0].models[2].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model3.pdb
fits[0].models[2].model_mw	8.789
fits[0].models[2].bead_radius	null
fits[0].models[2].log	null
fits[0].models[2].symmetry	null
fits[0].models[2].comment	null
fits[0].models[2].user	156
fits[0].models[3].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[3].software_version	null
fits[0].models[3].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model4.pdb
fits[0].models[3].model_mw	8.789
fits[0].models[3].bead_radius	null
fits[0].models[3].log	null
fits[0].models[3].symmetry	null
fits[0].models[3].comment	null
fits[0].models[3].user	156
fits[0].models[4].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[4].software_version	null
fits[0].models[4].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model5.pdb
fits[0].models[4].model_mw	8.789
fits[0].models[4].bead_radius	null
fits[0].models[4].log	null
fits[0].models[4].symmetry	null
fits[0].models[4].comment	null
fits[0].models[4].user	156
fits[0].models[5].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[5].software_version	null
fits[0].models[5].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model6.pdb
fits[0].models[5].model_mw	8.789
fits[0].models[5].bead_radius	null
fits[0].models[5].log	null
fits[0].models[5].symmetry	null
fits[0].models[5].comment	null
fits[0].models[5].user	156
fits[0].models[6].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[6].software_version	null
fits[0].models[6].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model7.pdb
fits[0].models[6].model_mw	8.789
fits[0].models[6].bead_radius	null
fits[0].models[6].log	null
fits[0].models[6].symmetry	null
fits[0].models[6].comment	null
fits[0].models[6].user	156
fits[0].models[7].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_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	atomic
fits[0].models[7].software_version	null
fits[0].models[7].model_data	https://www.sasbdb.org/media/pdb_file/SASDFJ9_fit1_model8.pdb
fits[0].models[7].model_mw	8.789
fits[0].models[7].bead_radius	null
fits[0].models[7].log	null
fits[0].models[7].symmetry	null
fits[0].models[7].comment	null
fits[0].models[7].user	156
fits[0].models[8].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDFJ9_fit1_model9_img.png
fits[0].models[8].software	Custom in-house
fits[0].models[8].pdb_link	[]
fits[0].models[8].model_title	null
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manifest.json：36 field values

Field path	Raw value
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View the complete summary.json source

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Title	Visualizing disordered single-stranded RNA: connecting sequence, structure and electrostatics.
Authors	Plumridge A, Andresen K, Pollack L
DOI / PMID	10.1021/jacs.9b04461 / 31804813