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{
"code": "SASDAT6",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4.",
"publication": {
"title": "Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4.",
"author_list": "Alonso-García N, García-Rubio I, Manso JA, Buey RM, Urien H, Sonnenberg A, Jeschke G, de Pereda JM",
"journal": "Acta Crystallogr D Biol Crystallogr",
"doi": "10.1107/S1399004715002485",
"pmid": "25849406",
"published_date": "2015 Apr"
},
"status": "released",
"submitted_date": "2014-11-12",
"released_date": "2015-07-07"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAT6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAT6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAT6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAT6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"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": "Integrin beta-4",
"short_name": null,
"sequence": "GSHMVPDTPTRLVFSALGPTSLRVSWQEPRCERPLQGYSVEYQLLNGGELHRLNIPNPAQTSVV\r\nVEDLLPN HSYVFRVRAQSQEGWGREREGVITIESQVHPQSPLCPLPGSAFTLSTPSAPG PLVFTALSPDSLQLSWERPRRPNGDIVGYLVTCEMAQGGGPATAFRVDGDSPESRLTVPG LSENVPYKFKVQARTTEGFGPEREGIITIES",
"organism": "Homo sapiens",
"uniprot_code": "P16144",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAGPRPSPWARLLLAALISVSLSGTLANRCKKAPVKSCTECVRVDKDCAYCTDEMFRDRR\nCNTQAELLAAGCQRESIVVMESSFQITEETQIDTTLRRSQMSPQGLRVRLRPGEERHFEL\nEVFEPLESPVDLYILMDFSNSMSDDLDNLKKMGQNLARVLSQLTSDYTIGFGKFVDKVSV\nPQTDMRPEKLKEPWPNSDPPFSFKNVISLTEDVDEFRNKLQGERISGNLDAPEGGFDAIL\nQTAVCTRDIGWRPDSTHLLVFSTESAFHYEADGANVLAGIMSRNDERCHLDTTGTYTQYR\nTQDYPSVPTLVRLLAKHNIIPIFAVTNYSYSYYEKLHTYFPVSSLGVLQEDSSNIVELLE\nEAFNRIRSNLDIRALDSPRGLRTEVTSKMFQKTRTGSFHIRRGEVGIYQVQLRALEHVDG\nTHVCQLPEDQKGNIHLKPSFSDGLKMDAGIICDVCTCELQKEVRSARCSFNGDFVCGQCV\nCSEGWSGQTCNCSTGSLSDIQPCLREGEDKPCSGRGECQCGHCVCYGEGRYEGQFCEYDN\nFQCPRTSGFLCNDRGRCSMGQCVCEPGWTGPSCDCPLSNATCIDSNGGICNGRGHCECGR\nCHCHQQSLYTDTICEINYSAIHPGLCEDLRSCVQCQAWGTGEKKGRTCEECNFKVKMVDE\nLKRAEEVVVRCSFRDEDDDCTYSYTMEGDGAPGPNSTVLVHKKKDCPPGSFWWLIPLLLL\nLLPLLALLLLLCWKYCACCKACLALLPCCNRGHMVGFKEDHYMLRENLMASDHLDTPMLR\nSGNLKGRDVVRWKVTNNMQRPGFATHAASINPTELVPYGLSLRLARLCTENLLKPDTREC\nAQLRQEVEENLNEVYRQISGVHKLQQTKFRQQPNAGKKQDHTIVDTVLMAPRSAKPALLK\nLTEKQVEQRAFHDLKVAPGYYTLTADQDARGMVEFQEGVELVDVRVPLFIRPEDDDEKQL\nLVEAIDVPAGTATLGRRLVNITIIKEQARDVVSFEQPEFSVSRGDQVARIPVIRRVLDGG\nKSQVSYRTQDGTAQGNRDYIPVEGELLFQPGEAWKELQVKLLELQEVDSLLRGRQVRRFH\nVQLSNPKFGAHLGQPHSTTIIIRDPDELDRSFTSQMLSSQPPPHGDLGAPQNPNAKAAGS\nRKIHFNWLPPSGKPMGYRVKYWIQGDSESEAHLLDSKVPSVELTNLYPYCDYEMKVCAYG\nAQGEGPYSSLVSCRTHQEVPSEPGRLAFNVVSSTVTQLSWAEPAETNGEITAYEVCYGLV\nNDDNRPIGPMKKVLVDNPKNRMLLIENLRESQPYRYTVKARNGAGWGPEREAIINLATQP\nKRPMSIPIIPDIPIVDAQSGEDYDSFLMYSDDVLRSPSGSQRPSVSDDTGCGWKFEPLLG\nEELDLRRVTWRLPPELIPRLSASSGRSSDAEAPHGPPDDGGAGGKGGSLPRSATPGPPGE\nHLVNGRMDFAFPGSTNSLHRMTTTSAAAYGTHLSPHVPHRVLSTSSTLTRDYNSLTRSEH\nSHSTTLPRDYSTLTSVSSHDSRLTAGVPDTPTRLVFSALGPTSLRVSWQEPRCERPLQGY\nSVEYQLLNGGELHRLNIPNPAQTSVVVEDLLPNHSYVFRVRAQSQEGWGREREGVITIES\nQVHPQSPLCPLPGSAFTLSTPSAPGPLVFTALSPDSLQLSWERPRRPNGDIVGYLVTCEM\nAQGGGPATAFRVDGDSPESRLTVPGLSENVPYKFKVQARTTEGFGPEREGIITIESQDGG\nPFPQLGSRAGLFQHPLQSEYSSITTTHTSATEPFLVDGLTLGAQHLEAGGSLTRHVTQEF\nVSRTLTTSGTLSTHMDQQFFQT",
"mw": 23.359,
"total_mw": 23.359,
"number_molecules": 1,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Sodium Phosphate 150 mM NaCl 5% glycerol 3 mM DTT",
"concentration_unit": "mM",
"comment": null,
"additive": "150 mM NaCl, 5% glycerol, 3 mM DTT",
"concentration": 20.0,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Integrin beta4, fragment of the cytoplasmic region encompassing the third and fourth FnIII domains",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "USAL",
"address": "Salamanca, Spain",
"full_name": "La Universidad de Salamanca",
"webpage": "http://www.usal.es"
}
],
"contributor_name": "Jose M",
"contributor_surname": "de Pereda",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2013-08-06",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": 1.5,
"concentration_max": 48.6,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.058,
"s_max": 3.491,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAT6_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAT6_fit1_model1.pdb",
"model_mw": 20.95,
"bead_radius": 1.5,
"log": null,
"symmetry": "",
"comment": "",
"user": 26
}
],
"fit_unit": "1/nm",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAT6_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.976836,
"p_value": 0.0,
"fit_residual_plot": "SASDAT6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAT6_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAT6_fit2_model1_img.png",
"software": "CRYSOL",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAT6_fit2_model1.pdb",
"model_mw": 23.19,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "",
"user": 26
}
],
"fit_unit": "1/nm",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAT6_fit2_fit_img.png",
"software": null,
"chi_square_value": 1.297321,
"p_value": 0.0,
"fit_residual_plot": "fit4columns178_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAT6_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM",
"i0_calibration_standard": null,
"description": "Combined use of SAXS, crystal structures, site directed spin labeling, double electron-electron resonance (DEER), and molecular modeling to analyze the structure of FnIII-3,4.",
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 19.2,
"experimental_mw_error": null,
"guinier_i0_mw": 19.2,
"guinier_i0_mw_error": null,
"porod_mw": 20.0,
"porod_mw_error": null,
"pddf_i0": 586.0,
"pddf_i0_error": null,
"guinier_i0": 590.0,
"guinier_i0_error": null,
"pddf_rg": 2.2,
"pddf_rg_error": null,
"guinier_rg": 2.2,
"guinier_rg_error": null,
"pddf_dmax": 7.0,
"pddf_dmax_error": null,
"porod_volume": 32.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": null,
"guinier_point_last": null,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDAT6_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
