{ "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", "submitted_date": "2024-08-29", "released_date": "2024-09-29" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVN6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVN6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVN6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVN6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVN6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVN6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVN6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger 4M", "resolution": 75.0 }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": null, "type_of_source": "X-ray synchrotron", "point_source": null, "line_collimation": null, "sample_path_length": null, "line_collimation_slitlength": null, "line_collimation_integrationwidth": null, "xray_energy": null, "beam_profile_ah": null, "beam_profile_al": null }, "sample": { "molecule": [ { "long_name": "Cereblon-midi", "short_name": "CRBNmidi", "sequence": "SAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPLQLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALIPTI", "organism": "synthetic construct", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 37.435, "total_mw": 37.435, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "CRBN-midi, an engineered Cereblon construct for crystallographic and biophysical studies of protein degraders (derived from human Cereblon, Uniprot Q96SW2)" } ], "buffer": { "name": "20 mM HEPES, 500 mM NaCl, 0.5 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Boc-VcN", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee", "webpage": null } ], "contributor_name": "Zoe", "contributor_surname": "Rutter", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2024-06-29", "storage_temperature": 15.0, "cell_temperature": 15.0, "exposure_time": 3.0, "number_of_frames": 600, "wavelength": 0.09464, "sample_detector_distance": 3.7, "concentration_min": null, "concentration_max": 3.4, "sample_volume": 50.0, "flow_rate": 0.08, "s_min": 0.045, "s_max": 3.4, "total_exposure_time": null, "seccolumn": 48 }, "fits": [], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "CRBN-midi, an engineered Cereblon construct for crystallographic and biophysical studies of protein degraders (derived from human Cereblon, Uniprot Q96SW2).", "experiment_description": "Synchrotron 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_unit": "arbitrary", "experimental_mw": 36.9, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 39.0, "porod_mw_error": null, "pddf_i0": 0.02076, "pddf_i0_error": null, "guinier_i0": 0.0207378, "guinier_i0_error": null, "pddf_rg": 2.37, "pddf_rg_error": null, "guinier_rg": 2.341, "guinier_rg_error": 0.051, "pddf_dmax": 9.1, "pddf_dmax_error": null, "porod_volume": 62.5, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 48, "guinier_point_last": 380, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVN6_datloglog_img.png", "symmetry": null, "last_modified": "2025-12-18T16:28:43.495264+01:00", "bragg_peak": [] }