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.
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{
"code": "SASDEY9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations",
"publication": {
"title": "Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations",
"author_list": "Solomon-Degefa H, Gebauer J, Jeffries C, Freiburg C, Meckelburg P, Bird L, Baumann U, Svergun D, Owens R, Werner J, Behrmann E, Paulsson M, Wagener R",
"journal": "Journal of Biological Chemistry",
"doi": "10.1074/jbc.RA120.014865",
"pmid": null,
"published_date": "2020 Jul 21"
},
"status": "released",
"submitted_date": null,
"released_date": "2020-07-25"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEY9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEY9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEY9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEY9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "Collagen, type VI, alpha 3",
"short_name": "N5N4",
"sequence": "GEKDVVFLIDGSEGVRSGFPLLKDFVQRVVESLDVGPDRVRVALVQYSDRTRPEFYLNSHMDQQGVISAIRRLTLLGGPT\r\nPNTGAALEFVLRNILTSSTGSRIAEGVPQLLIVLTAEPSGDDVRGPSVVLKQGGAVPIGIGIGNADISEMQTISFIPDFA\r\nVAIPTFRELGTIQQVISERVIQLNREELSSLKPILTPSTGAGVGSKKDVVFLIDGSRNAGPEFQYIRTLIERIVEYLDIG\r\nFDTTRVAVIQFSEDSKMEFPLNAHFSKDEVQNAVRRLRPKGGSQVYIGNALEYVLKNIFQRPLGSRIEEGVPQFLVLISS\r\nGKSDDEVDDSAVELKQFGVAPLTIARHTDQEELVKISLSPEYVYSVSTFRELPRLEQKLLTPITTLTSQQIHQILASTRY\r\nPPS",
"organism": "Mus musculus",
"uniprot_code": "D3YWD1",
"uniprot_range_first": 1023,
"uniprot_range_last": 1425,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MRKHRHLPLVAVFSLLLSGIATTHAQQHGDVKNGAAADIVFLVDSSWSAGKDRFLLVQEF\nLSDVVESLAVGDNDFHFALVRLNGNPHTEFLLNTYHSKQEVLSHIVNMSYIGGSNQTGKG\nLEYVIHSHLTEASGSRAADGVPQVIIVLTDGQSEDGFALPSAELKSADVNVFAVGVEGAD\nERALGEVASEPLSMHVFNLENVTSLHGLVGNLVSCIHSSVNPERAGDKESLKDITAQDSA\nDIIFLIDGSQNTGNANFDVIRDFLVNVLERLSVGNQQVQVGVVQYSEEPITMFSLNSYPS\nKAAVLDAVKGLSLVGGESANIGQALDFVVENHFTRAGGSRVEEGVPQVLVLISAGPSSDE\nIRDSVVALKQASVFSFGLGAQAASRAELQHIATDDSLVFTVPEFRSFGDLQEQILPYLVG\nVAQRHIVLQPPAIVTQVMEVNKRDIVFLVDGSSSLGPSNFNAIRDFVTRVIQRLEIGQDL\nVQVSVAQYADTVKPEFYLNSYTNKRDAITAVRKMRALNGSALYTGSSLDFVRNNLFTSSA\nGHRAAEGVPKLLVLITGGKSLDEVSQPAQELKRGSIMALAVGSKAADEDELKEIAFDSSL\nVFIPAEFRPAPLQNMLPSLMAPLRTLTGTTEVHVNKRDIIFLLDGSDNVGKNNFPYVRDF\nVTNLVNSLDVGSDNIRVGLVQFSDTPVTEFSLDTYQTKSELLAHLRRLQLKGGSGLNAGS\nALSYIHANHFTEAGGSRTREHVPQLLLLLMAGPSEDAYLQAANALVRSGVLTFCVGTNRA\nDKAELEHIAFNPSLVYLMDDFRSLPSLPQQLIQPLTTYVSGGVQEVPLSQPESKRDILFL\nFDGSVNVLGQFPAVRDFLYRIIEELDVKPDGTRVAIAQFSDDVRLESRFSEHQTKAEILN\nLVKKMKLKTGKALNLGYALDYALRNIFVRSAGSRIEDNVQQFLVLLVAGRSSDAVAGPAS\nSLKQRGVVPFIFQAKNANPSELEQIVLSPAFILAAESLPKIGDLQSQIVSLLKAEQGSGP\nVSGEKDVVFLIDGSEGVRSGFPLLKDFVQRVVESLDVGPDRVRVALVQYSDRTRPEFYLN\nSHMDQQGVISAIRRLTLLGGPTPNTGAALEFVLRNILTSSTGSRIAEGVPQLLIVLTAEP\nSGDDVRGPSVVLKQGGAVPIGIGIGNADISEMQTISFIPDFAVAIPTFRELGTIQQVISE\nRVIQLNREELSSLKPILTPSTGAGVGSKKDVVFLIDGSRNAGPEFQYIRTLIERIVEYLD\nIGFDTTRVAVIQFSEDSKMEFPLNAHFSKDEVQNAVRRLRPKGGSQVYIGNALEYVLKNI\nFQRPLGSRIEEGVPQFLVLISSGKSDDEVDDSAVELKQFGVAPLTIARHTDQEELVKISL\nSPEYVYSVSTFRELPRLEQKLLTPITTLTSQQIHQILASTRYPPSVVESDAADIVFLIDS\nSDAVKPDGIAHIRDFVSRIVRRLNIGPSKVRIGVVQFSNDVFPEFYLKTHKSQSSVLEAI\nRRLRFKGGSPLNTGRALEFVARNLFVKSAGSRIEDGVPQHLVLFLGGKSQDDVARHAQVI\nSSSGIVSLGIGDRNIDRTDLQTITNDPRLVFTVREFRELPNIEERVMLSFGPSGATPQPP\nGVDLPSPSRPEKKKADIVFLLDGSINFRRDSFQEVLRFASEIVDTVYEDGDSIRVGLVQY\nNSDPTDEFFLRDFSTKRQIIDAI",
"mw": 44.274,
"total_mw": 44.274,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM TRIS, 150mM NaCl 3% v/v glycerol",
"concentration_unit": null,
"comment": "The TRIS buffer is pH first, then add additional components are added without further pH adjustment",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Collagen VI von Willebrand factor (VWA) double-domain fragment, N5N4",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-04-20",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 18,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 12.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.068,
"s_max": 6.998,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY9_fit1_model1_img.png",
"software": "DAMMIN",
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"software_version": "DAMMIN",
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"model_mw": 39.314,
"bead_radius": 2.5,
"log": null,
"symmetry": "P1",
"comment": "Refined individual model calculated from 10 spatially aligned models",
"user": 9
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY9_fit1_model2_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
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"software_version": "5.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEY9_fit1_model2.pdb",
"model_mw": 37.987,
"bead_radius": 2.5,
"log": null,
"symmetry": "P1",
"comment": "Averaged spatial repersentation calculated from 10 aligned individual models",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEY9_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.027,
"p_value": 0.852619,
"fit_residual_plot": "SASDEY9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY9_fit1.fir",
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},
{
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"log": null,
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"user": 9
}
],
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"software": "GASBOR",
"chi_square_value": 1.02,
"p_value": 0.798665,
"fit_residual_plot": "SASDEY9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY9_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/n.log",
"software_version": "2.3i",
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},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY9_fit3_model1_img.png",
"software": "BUNCH",
"pdb_link": [
{
"pdb_code": "4igi",
"ext_code": "4IGI",
"ext_type": "pdb",
"difference_with_model": "derived"
}
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"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEY9_fit3_model1.pdb",
"model_mw": 44.36,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Generated using the crystal structure of N5 in combination with an ITASSER homology model of N4",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEY9_fit3_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.018,
"p_value": 0.180377,
"fit_residual_plot": "SASDEY9_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY9_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/XF00.log",
"software_version": "2.8.3",
"description": ""
},
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEY9_fit4_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.037,
"p_value": 0.1753,
"fit_residual_plot": "SASDEY9_fit4_fitresiduals_img.png",
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"fit_log": null,
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}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of the collagen VI N5N4 double-domain fragment in 20 mM Tris, pH 7.4, 150mM NaCl 3% v/v glycerol, were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) equipped with a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20°C using the following parameters: Column: GE-Healthcare S75 Increase 10/300 analytical SEC column; Flow rate: 0.6 mL/min; Sample injection concentration: 12.0 mg/mL; Injection volume: 55 μL. Total X-ray acquisition time = 2400 s. The data were collected through the SEC peak of the protein as a series of 18 x 1 second exposures and processed using CHROMIXS (Panjkovich & Svergun, 2018 Bioinformatics 34(11):1944-1946) that was also used to select an appropriate matched solvent-blank. Parallel inline multi-angle laser and dynamic light scattering with refractive index measurements (SEC-MALLS/DLS/RI) were performed using a Wyatt Mini-Dawn TREOS with an in-built quasi elastic light scattering (QELS) module coupled to an OptiLab T-Rex refractometer. The quoted experiential MW for this entry is derived from MALLS. Concentration-independent MW estimates obtained directly from the SAXS data using DATMW (Hajizadeh et al., 2018 Scientific Reports 8, 7204), as part of CHROMIXS/ATSAS 2.8.3, as well as the SEC-MALLS/DLS/RI data and additional modelling files, including ITASSER homology modelling (Yang et al., 2015 Nature Methods 12, 7-8) are included in the full-entry zip archive.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 43.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 41.0,
"porod_mw_error": null,
"pddf_i0": 287.2,
"pddf_i0_error": null,
"guinier_i0": 286.77,
"guinier_i0_error": 0.42,
"pddf_rg": 2.895,
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"guinier_rg_error": 0.01,
"pddf_dmax": 9.85,
"pddf_dmax_error": null,
"porod_volume": 66.2,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 122,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEY9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:55:24.740692+02:00",
"bragg_peak": []
}
