SASDDR5

Human metaphase chromosomes in 5 mM magnesium chloride

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-12-07T16:12:46.422621+01:00

Note: As the sample used for the SAXS measurements consists of intact chromosomes, the MW, Rg and sample concentration cannot be determined. Although the data for this entry are displayed as logI(s) vs s, by convention in the field a plot of log(I(s)s^2) vs s is used. This transformed I(s) data is included as an additional file in the full entry zip archive.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Human metaphase chromosomes in 5 mM magnesium chloride

Concentration— – — Buffer / pH10 mM PIPES, 5 mM magnesium chloride, 10 mM sodium chloride, 120 mM potassium chloride, 40% glycerol / 7.2
Experimental temperature25.0 Facility / beamlineALBA / BL11 - NCD
Wavelength0.129 nmExposure60.0 s × 1

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Human metaphase chromosomes in 5 mM magnesium chloride
View sequence
GGG
otherHomo sapiens——–—monomerMolecule count 10.001 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11511[2]0.00105–3.173 1/nmNo uncertainty columnMissing 15110sasbdb/entries/r5/sasddr5/source/SASDDR5.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
mwExperimental0.0—kDa
rgP(r)3.0—nm

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

This entry has no source fit record.

▶

4. Source File Index Source Files

▶

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 name10 mM PIPES, 5 mM magnesium chloride, 10 mM sodium chloride, 120 mM potassium chloride, 40% glycerolBuffer concentration—
pH7.2Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-06-06Storage / measurement temperature— / 25.0
Exposure time60.0Frames1
Wavelength0.129Sample-to-detector distance2.61
SourceX-ray synchrotronDetectorADSC Quantum 210r
Facility / beamlineALBA / BL11 - NCD · Cerdanyola del Vallès, Barcelona, Spain
q range0.001 – 3.173Sample 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

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:134 field values
Field pathRaw value
codeSASDDR5
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
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project.publication.titleFrozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.
project.publication.author_listChicano A, Crosas E, Otón J, Melero R, Engel BD, Daban JR
project.publication.journalEMBO J
project.publication.doi10.15252/embj.201899769
project.publication.pmid30609992
project.publication.published_date2019 Apr 1
project.statusreleased
project.submitted_date2018-03-30
project.released_date2023-12-07
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experiment.instrument.countrySpain
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experiment.sample.molecule[0].long_nameHuman metaphase chromosomes in 5 mM magnesium chloride
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceGGG
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
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experiment.sample.molecule[0].uniprot_sequencenull
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experiment.sample.molecule[0].total_mw0.001
experiment.sample.molecule[0].number_molecules1
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experiment.sample.molecule[0].deuterationnull
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experiment.sample.molecule[0].molecule_descriptionnull
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experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.2
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameHuman metaphase chromosomes in 5 mM magnesium chloride
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
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experiment.sample.dry_volnull
experiment.sample.absorbptionnull
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experiment.contributor[0].affiliation[0].webpagehttp://www.desy.de/
experiment.contributor[0].contributor_nameEva
experiment.contributor[0].contributor_surnameCrosas
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-06-06
experiment.storage_temperaturenull
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experiment.exposure_time60.0
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experiment.concentration_minnull
experiment.concentration_maxnull
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experiment.flow_ratenull
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fits[]
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pddf_softwarenull
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i0_calibration_standardnull
descriptionNote: As the sample used for the SAXS measurements consists of intact chromosomes, the MW, Rg and sample concentration cannot be determined. Although the data for this entry are displayed as logI(s) vs s, by convention in the field a plot of log(I(s)s^2) vs s is used. This transformed I(s) data is included as an additional file in the full entry zip archive.
experiment_descriptionSynchrotron SAXS data from solutions of human metaphase chromosomes in 5 mM magnesium chloride, 10 mM PIPES, 10 mM sodium chloride, 120 mM potassium chloride, 40 %v/v glycerol, pH 7.2 were collected on the BL11-NCD beam line at the ALBA storage ring (Cerdanyola del Vallès, Barcelona, Spain) using a CCD ADSC Quantum 210r detector at a sample-detector distance of 2.6 m and at a wavelength of λ = 0.129 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Sample data were collected at 25°C. One 60 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
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experimental_mw_errornull
guinier_i0_mwnull
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guinier_point_lastnull
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pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDDR5_datloglog_img.png
symmetrynull
last_modified2023-12-07T16:12:46.422621+01:00
bragg_peak[]
manifest.json:33 field values
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codeSASDDR5
statussuccess
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View the complete summary.json source
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View the complete manifest.json source
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