SASDVN6

Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Boc-VcN

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2025-12-18T16:28:43.495264+01:00

CRBN-midi, an engineered Cereblon construct for crystallographic and biophysical studies of protein degraders (derived from human Cereblon, Uniprot Q96SW2).

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Boc-VcN

Concentration— – 3.4 Buffer / pH20 mM HEPES, 500 mM NaCl, 0.5 mM TCEP / 7.5
Experimental temperature15.0 Facility / beamlineDiamond Light Source / B21
Wavelength0.09464 nmExposure3.0 s × 600

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Cereblon-midi
View sequence
SAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPLQLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALIPTI
proteinsynthetic construct——–—monomerMolecule count 137.435 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12573[3]0.0045–0.34 1/AHas uncertainty columnMissing 0212sasbdb/entries/n6/sasdvn6/source/SASDVN6.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)9.1—Å
i0Guinier0.0207378—arbitrary
i0P(r)0.02076—arbitrary
mwExperimental36.9—kDa
mwPorod39.0—kDa
porod_volumePorod62.5—ų
rgGuinier2.3410.051Å
rgP(r)2.37—Å

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.

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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 name20 mM HEPES, 500 mM NaCl, 0.5 mM TCEPBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2024-06-29Storage / measurement temperature15.0 / 15.0
Exposure time3.0Frames600
Wavelength0.09464Sample-to-detector distance3.7
SourceX-ray synchrotronDetectorEiger 4M
Facility / beamlineDiamond Light Source / B21 · Didcot, UK
q range0.045 – 3.4Sample volume / flow rate50.0 / 0.08

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:134 field values
Field pathRaw value
codeSASDVN6
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleDesign of a Cereblon construct for crystallographic and biophysical studies of protein degraders
project.publication.titleDesign of a Cereblon construct for crystallographic and biophysical studies of protein degraders
project.publication.author_listKroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A
project.publication.journalNature Communications
project.publication.doi10.1038/s41467-024-52871-9
project.publication.pmidnull
project.publication.published_date2024 Oct 15
project.statusreleased
project.submitted_date2024-08-29
project.released_date2024-09-29
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experiment.instrument.detector.typenull
experiment.instrument.detector.nameEiger 4M
experiment.instrument.detector.resolution75.0
experiment.instrument.nameDiamond Light Source
experiment.instrument.cityDidcot
experiment.instrument.countryUK
experiment.instrument.beamline_nameB21
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameCereblon-midi
experiment.sample.molecule[0].short_nameCRBNmidi
experiment.sample.molecule[0].sequenceSAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPLQLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALIPTI
experiment.sample.molecule[0].organismsynthetic construct
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_typeprotein
experiment.sample.molecule[0].uniprot_sequence
experiment.sample.molecule[0].mw37.435
experiment.sample.molecule[0].total_mw37.435
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_descriptionCRBN-midi, an engineered Cereblon construct for crystallographic and biophysical studies of protein degraders (derived from human Cereblon, Uniprot Q96SW2)
experiment.sample.buffer.name20 mM HEPES, 500 mM NaCl, 0.5 mM TCEP
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameCereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Boc-VcN
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].addressnull
experiment.contributor[0].affiliation[0].full_nameBiological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameZoe
experiment.contributor[0].contributor_surnameRutter
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2024-06-29
experiment.storage_temperature15.0
experiment.cell_temperature15.0
experiment.exposure_time3.0
experiment.number_of_frames600
experiment.wavelength0.09464
experiment.sample_detector_distance3.7
experiment.concentration_minnull
experiment.concentration_max3.4
experiment.sample_volume50.0
experiment.flow_rate0.08
experiment.s_min0.045
experiment.s_max3.4
experiment.total_exposure_timenull
experiment.seccolumn48
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionCRBN-midi, an engineered Cereblon construct for crystallographic and biophysical studies of protein degraders (derived from human Cereblon, Uniprot Q96SW2).
experiment_descriptionSynchrotron SAXS data from solutions of CRBNmidi bound to Boc-VcN in 20 mM HEPES, 500 mM NaCl, 0.5 mM TCEP, pH 7.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.09464 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 3.4 mg/ml was injected at a 0.08 ml/min flow rate onto a Cytiva Superdex 200 Increase 3.2/300 column at 15°C. 600 successive 3 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.
tags[]
intensity_unitarbitrary
experimental_mw36.9
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
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porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first48
guinier_point_last380
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDVN6_datloglog_img.png
symmetrynull
last_modified2025-12-18T16:28:43.495264+01:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDVN6
statussuccess
started_at2026-08-11T15:13:21.428784+00:00
finished_at2026-08-11T15:13:30.215657+00:00
source_last_modified2025-12-18T16:28:43.495264+01:00
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View the complete summary.json source
{
  "code": "SASDVN6",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders",
    "publication": {
      "title": "Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders",
      "author_list": "Kroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A",
      "journal": "Nature Communications",
      "doi": "10.1038/s41467-024-52871-9",
      "pmid": null,
      "published_date": "2024 Oct 15"
    },
    "status": "released",
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    "released_date": "2024-09-29"
  },
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  "tags": [],
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View the complete manifest.json source
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