SASDDG7

Armless mitochondrial tRNA-Ile from Romanomermis culicivorax

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2019-12-06T13:07:15.624532+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Armless mitochondrial tRNA-Ile from Romanomermis culicivorax

Concentration— – — Buffer / pH50 mM HEPES-NaOH 10 mM MgCl2 / 7.4
Experimental temperature15.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1033 nmExposure1.0 s × 240

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Isoleucyl transfer RNA
View sequence
>TRNAILE_R.CULICIVORAXCUUAAUAGAGAACAAUUUAAAUUGAUAAUUUAAAUUAAAAUUUAAGA
RNARomanomermis culicivorax——–—monomerMolecule count 115.115 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1667[3]0.00624746–0.400321 1/AHas uncertainty columnMissing 00sasbdb/entries/g7/sasddg7/source/SASDDG7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)6.74—Å
i0Guinier0.017484e-05arbitrary
i0P(r)0.017582e-05arbitrary
mwExperimental14.8—kDa
porod_volumePorod19.7—ų
rgGuinier2.030.007Å
rgP(r)2.090.004Å

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

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3. Source Fits and Models Source Fits & Models

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4. Source File Index Source Files

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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 name50 mM HEPES-NaOH 10 mM MgCl2Buffer concentration—
pH7.4Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-12-16Storage / measurement temperature4.0 / 15.0
Exposure time1.0Frames240
Wavelength0.1033Sample-to-detector distance2.8
SourceX-ray synchrotronDetectorAVIEX PCCD170170
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.062 – 4.003Sample volume / flow rate— / —

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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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:156 field values
Field pathRaw value
codeSASDDG7
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleSmall but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax.
project.publication.titleSmall but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax.
project.publication.author_listJühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, Betat H, Sauter C, Mörl M
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gky593
project.publication.pmid29986062
project.publication.published_date2018 Jul 9
project.statusreleased
project.submitted_date2018-05-29
project.released_date2018-08-01
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experiment.instrument.detector.nameAVIEX PCCD170170
experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameIsoleucyl transfer RNA
experiment.sample.molecule[0].short_nametRNA-Ile
experiment.sample.molecule[0].sequence>tRNAile_R.culicivorax CUUAAUAGAGAACAAUUUAAAUUGAUAAUUUAAAUUAAAAUUUAAGA
experiment.sample.molecule[0].organismRomanomermis culicivorax
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeRNA
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw15.115
experiment.sample.molecule[0].total_mw15.115
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name50 mM HEPES-NaOH 10 mM MgCl2
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameArmless mitochondrial tRNA-Ile from Romanomermis culicivorax
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressFrance
experiment.contributor[0].affiliation[0].full_nameIBMC - CNRS
experiment.contributor[0].affiliation[0].webpagehttp://www-ibmc.u-strasbg.fr/
experiment.contributor[0].contributor_nameClaude
experiment.contributor[0].contributor_surnameSauter
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-8766-287X
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-12-16
experiment.storage_temperature4.0
experiment.cell_temperature15.0
experiment.exposure_time1.0
experiment.number_of_frames240
experiment.wavelength0.1033
experiment.sample_detector_distance2.8
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experiment.concentration_maxnull
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experiment.flow_ratenull
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fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].lognull
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fits[0].softwareCRYSOL
fits[0].chi_square_value1.659
fits[0].p_value0.0
fits[0].fit_residual_plotSASDDG7_fit1_fitresiduals_img.png
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fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of mitochondrial tRNA-Ile were performed at the SWING beam line (SOLEIL synchrotron, Saint-Aubin, France) equipped with a 17 x 17 cm2 low-noise Aviex CCD detector at a sample-detector distance of 2.8 m using an X-ray wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The tRNA-Ile sample was concentrated to 3.5 mg/ml in 200 µl buffer containing 50 mM HEPES-NaOH, pH 7.4, and 10 mM MgCl2 using centrifugation in an Amicon Ultra-4 (cut off 3 kDa). 70 µl of solution were loaded onto a size exclusion chromatography (SEC) HPLC column (BioSEC3-150, Agilent) upstream the SAXS cell in order to separate monomers from potential oligomers and aggregates. SEC elution was performed using an Agilent HPLC system at 0.2 ml/min in 50 mM HEPES-NaOH, pH 7.4, and 10 mM MgCl2 at 15°C. Samples were exposed to X-rays directly downstream to the SEC column to record the corresponding scattering signal (240 images of 1 sec exposure at 0.5 sec interval). The scattering signal from the buffer was collected at the beginning of the run (90 images) to be subtracted from the RNA signal. SAXS images were processed with FOXTROT (David & Pérez, 2009) to generate individual curves (subtracted from the buffer signal) and plots corresponding to I(0) and gyration radius Rg as a function of frames. US-SOMO (Brookes et al, 2016) was used to separate the scattering signal corresponding of successive molecular species in overlapping regions of the chromatogram by Gaussian decomposition and curves from consecutive images showing similar Rg were averaged. Resulting SAXS profiles were analyzed with the package ATSAS 2.8.2 (Franke et al, 2017) to evaluate structural parameters such as radius of gyration Rg from Guinier plots (PRIMUS; Konarev et al, 2003), as well as the particle distance distribution function p(r) (GNOM; Svergun, 1992) and associated maximum distance Dmax and Porod volume.
tags[]
intensity_unitarbitrary
experimental_mw14.8
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.01758
pddf_i0_error2e-05
guinier_i00.01748
guinier_i0_error4e-05
pddf_rg2.09
pddf_rg_error0.004
guinier_rg2.03
guinier_rg_error0.007
pddf_dmax6.74
pddf_dmax_errornull
porod_volume19.7
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first43
guinier_point_last93
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDDG7_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDDG7
statussuccess
started_at2026-08-11T15:29:17.937245+00:00
finished_at2026-08-11T15:29:26.404031+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
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  "status": "Published",
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  "angular_unit": "1/A",
  "project": {
    "title": "Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax.",
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      "title": "Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax.",
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      "journal": "Nucleic Acids Res",
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  "experiment_description": "Synchrotron SAXS data from solutions of mitochondrial tRNA-Ile were performed at the SWING beam line (SOLEIL synchrotron, Saint-Aubin, France) equipped with a 17 x 17 cm2 low-noise Aviex CCD detector at a sample-detector distance of 2.8 m using an X-ray wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The tRNA-Ile sample was concentrated to 3.5 mg/ml in 200 µl buffer containing 50 mM HEPES-NaOH, pH 7.4, and 10 mM MgCl2 using centrifugation in an Amicon Ultra-4 (cut off 3 kDa). 70 µl of solution were loaded onto a size exclusion chromatography (SEC) HPLC column (BioSEC3-150, Agilent) upstream the SAXS cell in order to separate monomers from potential oligomers and aggregates. SEC elution was performed using an Agilent HPLC system at 0.2 ml/min in 50 mM HEPES-NaOH, pH 7.4, and 10 mM MgCl2 at 15°C. Samples were exposed to X-rays directly downstream to the SEC column to record the corresponding scattering signal (240 images of 1 sec exposure at 0.5 sec interval). The scattering signal from the buffer was collected at the beginning of the run (90 images) to be subtracted from the RNA signal. SAXS images were processed with FOXTROT (David & Pérez, 2009) to generate individual curves (subtracted from the buffer signal) and plots corresponding to I(0) and gyration radius Rg as a function of frames. US-SOMO (Brookes et al, 2016) was used to separate the scattering signal corresponding of successive molecular species in overlapping regions of the chromatogram by Gaussian decomposition and curves from consecutive images showing similar Rg were averaged. Resulting SAXS profiles were analyzed with the package ATSAS 2.8.2 (Franke et al, 2017) to evaluate structural parameters such as radius of gyration Rg from Guinier plots (PRIMUS; Konarev et al, 2003), as well as the particle distance distribution function p(r) (GNOM; Svergun, 1992) and associated maximum distance Dmax and Porod volume.",
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  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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View the complete manifest.json source
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