The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDUV5",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.",
"publication": {
"title": "A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.",
"author_list": "Tripepi A, Shakoor H, Klapetek P",
"journal": "Curr Protoc",
"doi": "10.1002/cpz1.70084",
"pmid": "39781608",
"published_date": "2025 Jan"
},
"status": "released",
"submitted_date": "2024-03-22",
"released_date": "2025-01-14"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUV5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUV5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUV5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUV5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Hybrid Photon Counting (HPC) X-ray detector",
"name": "Rigaku HyPix-3000",
"resolution": 100.0
},
"name": "CEITEC",
"city": "Brno",
"country": "Czech Republic",
"beamline_name": "Rigaku BioSAXS-2000",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "3'UTR fragment of ADP-ribosylation factor 1",
"short_name": "ARF1",
"sequence": "GGAGUGCCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGGUACUCC",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "RNA",
"uniprot_sequence": "",
"mw": 14.185,
"total_mw": 14.185,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
},
{
"long_name": "Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM)",
"short_name": "Stau1dsRBD3endΔSSM",
"sequence": "GSHMEENLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIEKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS\r\nITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF\r\nPVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN\r\nLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN\r\nAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE\r\nKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ\r\nPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM\r\nVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH\r\nVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES\r\nCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC",
"mw": 40.674,
"total_mw": 81.348,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The protein construct used for SAXS contains three additional non-native amino acids at the N-terminus (GSH)."
}
],
"buffer": {
"name": "50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to 3'UTR fragment of ADP-ribosylation factor 1",
"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": "CEITEC - Central European Institute of Technology, Masaryk University",
"webpage": "https://www.ceitec.eu/"
}
],
"contributor_name": "Tomas",
"contributor_surname": "Klumpler",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-01-12",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 3600.0,
"number_of_frames": 1,
"wavelength": 0.154,
"sample_detector_distance": 0.48,
"concentration_min": null,
"concentration_max": 3.2,
"sample_volume": 100.0,
"flow_rate": 0.6,
"s_min": 0.1,
"s_max": 4.007,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV5_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "ATSAS 2.8.4 (r10552)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV5_fit1_model1.pdb",
"model_mw": 93.38,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 195
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV5_fit1_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.11,
"p_value": 0.0549,
"fit_residual_plot": "SASDUV5_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV5_fit1.fit",
"fit_log": null,
"software_version": "ATSAS 2.8.4 (r10552)",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "SAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to the 3'UTR fragment of ADP-ribosylation factor 1 in 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH 7 were collected using a Rigaku BioSAXS-2000 instrument at CEITEC (Brno, Czech Republic) equipped with a Rigaku HyPix-3000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.20 mg/ml was measured at 20°C. One 3600 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": [],
"intensity_unit": "arbitrary",
"experimental_mw": 109.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 86.9,
"porod_mw_error": null,
"pddf_i0": 0.5567,
"pddf_i0_error": null,
"guinier_i0": 0.585799,
"guinier_i0_error": null,
"pddf_rg": 5.32,
"pddf_rg_error": null,
"guinier_rg": 5.471,
"guinier_rg_error": 2.253,
"pddf_dmax": 16.12,
"pddf_dmax_error": null,
"porod_volume": 139.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 17,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDUV5_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-01-14T14:00:42.833878+01:00",
"bragg_peak": []
}View the complete manifest.json source
{
"code": "SASDUV5",
"status": "success",
"started_at": "2026-08-11T16:40:26.829095+00:00",
"finished_at": "2026-08-11T16:40:34.419788+00:00",
"source_last_modified": "2025-01-14T14:00:42.833878+01:00",
"files": [
{
"status": "downloaded",
"url": "https://www.sasbdb.org/rest-api/entry/summary/SASDUV5/",
"path": "/data/saxsdb/sasbdb/entries/v5/sasduv5/source/summary.json",
"size": 9105,
"sha256": "c464cfd8ba0552a52c2bd21a07e498a2c0f0c65a2c72711039c3ae44aeac1786"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/intensities_files/SASDUV5.dat",
"path": "/data/saxsdb/sasbdb/entries/v5/sasduv5/source/SASDUV5.dat",
"size": 14802,
"sha256": "83a3204e122aabf4b3fe06b4ff3815ecc3e43ea37048c71a738c1a6687173c85",
"role": "curve"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/p_of_R_files/SASDUV5.out",
"path": "/data/saxsdb/sasbdb/entries/v5/sasduv5/source/SASDUV5.out",
"size": 19724,
"sha256": "953ad44e1decf02f823dcfb340c53539c687452d455ffe0f8e72960a3ca9917b",
"role": "pddf"
},
{
"status": "not_available",
"url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUV5.sascif",
"path": "/data/saxsdb/sasbdb/entries/v5/sasduv5/source/SASDUV5.sascif",
"role": "sascif"
},
{
"status": "downloaded",
"url": "https://www.sasbdb.org/media/zip_directories/SASDUV5.zip",
"path": "/data/saxsdb/sasbdb/entries/v5/sasduv5/source/SASDUV5.zip",
"size": 93624,
"sha256": "8fd5fd6e031860b48e03b30bab45526d5b2a1474db7523055bf6ef0bad69ebb0",
"role": "full_entry_zip",
"zip_member_count": 4,
"zip_validation": "central_directory_readable"
}
]
}
