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{
"code": "SASDEZ9",
"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/SASDEZ9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEZ9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEZ9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEZ9.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": "N6N3",
"sequence": "MAHHHHHHSSGSWSHPQFEKGGGSGGGSGGGSWSHPQFEKSSGLEVLFQGP\r\nESKRDILFLFDGSVNVLGQFPAVRDFLYRIIEELDVKPDGTRVAIAQFSD\r\nDVRLESRFSEHQTKAEILNLVKKMKLKTGKALNLGYALDYALRNIFVRSA\r\nGSRIEDNVQQFLVLLVAGRSSDAVAGPASSLKQRGVVPFIFQAKNANPSE\r\nLEQIVLSPAFILAAESLPKIGDLQSQIVSLLKAEQGSGPVSGEKDVVFLI\r\nDGSEGVRSGFPLLKDFVQRVVESLDVGPDRVRVALVQYSDRTRPEFYLNS\r\nHMDQQGVISAIRRLTLLGGPTPNTGAALEFVLRNILTSSTGSRIAEGVPQ\r\nLLIVLTAEPSGDDVRGPSVVLKQGGAVPIGIGIGNADISEMQTISFIPDF\r\nAVAIPTFRELGTIQQVISERVIQLNREELSSLKPILTPSTGAGVGSKKDV\r\nVFLIDGSRNAGPEFQYIRTLIERIVEYLDIGFDTTRVAVIQFSEDSKMEF\r\nPLNAHFSKDEVQNAVRRLRPKGGSQVYIGNALEYVLKNIFQRPLGSRIEE\r\nGVPQFLVLISSGKSDDEVDDSAVELKQFGVAPLTIARHTDQEELVKISLS\r\nPEYVYSVSTFRELPRLEQKLLTPITTLTSQQIHQILASTRYPPSVVESDA\r\nADIVFLIDSSDAVKPDGIAHIRDFVSRIVRRLNIGPSKVRIGVVQFSNDV\r\nFPEFYLKTHKSQSSVLEAIRRLRFKGGSPLNTGRALEFVARNLFVKSAGS\r\nRIEDGVPQHLVLFLGGKSQDDVARHAQVISSSGIVSLGIGDRNIDRTDLQ\r\nTITNDPRLVFTVREFRELPNIEERVMLSFGPSGATPQPPGVDLPSPSRP",
"organism": "Mus musculus",
"uniprot_code": "D3YWD1",
"uniprot_range_first": 831,
"uniprot_range_last": 1630,
"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": 92.936,
"total_mw": 92.936,
"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) four-domain fragment, N6N3",
"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": "2018-11-04",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 50,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 7.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.061,
"s_max": 7.003,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "4igi",
"ext_code": "4IGI",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "5",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit1_model1.pdb",
"model_mw": 93.59,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/07N6N3.log",
"symmetry": "P1",
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.02,
"p_value": 0.553966,
"fit_residual_plot": "SASDEZ9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/07N6N300.log",
"software_version": "2.8.3",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit2_model1_img.png",
"software": "BUNCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "8",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit2_model1.pdb",
"model_mw": 93.57,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/N6N3Q.log",
"symmetry": "P1",
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.046,
"p_value": 0.093444,
"fit_residual_plot": "SASDEZ9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/N6N3Q00.log",
"software_version": "2.8.3",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ9_fit3_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ9_fit3_model1.pdb",
"model_mw": null,
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"log": null,
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"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit3_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 0.98,
"p_value": 0.863635,
"fit_residual_plot": "SASDEZ9_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit3.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/N6B.log",
"software_version": "2.3i",
"description": ""
},
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEZ9_fit4_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 0.975,
"p_value": 0.8998,
"fit_residual_plot": "SASDEZ9_fit4_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ9_fit4.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_cw2kJv9.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Collagen VI von Willebrand factor (VWA) four-domain fragment, N6N3 in 20 mM TRIS, 150mM NaCl 3% v/v glycerol, pH 7.4 were collected on the EMBL P12 camera at the PETRA III storage ring (Hamburg, Germany) using 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 S200 Increase 10/300 analytical SEC column; Flow rate: 0.6 mL/min; Sample injection concentration: 7 mg/mL; Injection volume: 75 μL. Total X-ray acquisition time = 2400 s. The data were collected through the SEC peak of the protein as a series of 50 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": 89.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 89.0,
"porod_mw_error": null,
"pddf_i0": 517.8,
"pddf_i0_error": null,
"guinier_i0": 514.54,
"guinier_i0_error": 1.1,
"pddf_rg": 4.24,
"pddf_rg_error": null,
"guinier_rg": 4.12,
"guinier_rg_error": 0.01,
"pddf_dmax": 15.6,
"pddf_dmax_error": null,
"porod_volume": 143.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 93,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEZ9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:55:24.740692+02:00",
"bragg_peak": []
}
