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": "SASDDY2",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.",
"publication": {
"title": "The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.",
"author_list": "Karki S, Paudel P, Sele C, Shkumatov AV, Kajander T",
"journal": "Protein Eng Des Sel",
"doi": "10.1093/protein/gzy012",
"pmid": "29897575",
"published_date": "2018 Jun 12"
},
"status": "released",
"submitted_date": "2018-01-11",
"released_date": "2018-06-13"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDY2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDY2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDY2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDY2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDY2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDY2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDY2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"beam_geometry": "",
"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": "Leucine-rich repeat and fibronectin type-III domain-containing protein 4",
"short_name": "LRR-Ig",
"sequence": "CPLPCVCQNLSESLSTLCAHRGLLFVPPNVDRRTVELRLADNFIQALGPPDFRNMTGLVDLTLSRNAITRIGARSFGDLE\r\nSLRSLHLDGNRLVELGSSSLRGPVNLQHLILSGNQLGRIAPGAFDDFLDSLEDLDVSYNNLRQVPWAGIGSMPALHTLNL\r\nDHNLIDALPPGVFAQLSQLSRLDLTSNRLATLAPDPLFSRGRDAEASPSPLVLSFSGNPLHCNCELLWLRRLARPDDLET\r\nCASPPTLAGRYFWAVPEGEFSCEPPLIARHTQRLWVLEGQRATLRCRALGDPVPTMHWVGPDDRLVGNSSRAWAFPNGTL\r\nEIGVTGAGDAGAYTCIATNPAGEATARVELRVLALGTRGSEVLFQ",
"organism": "Mus musculus",
"uniprot_code": "Q80XU8",
"uniprot_range_first": 17,
"uniprot_range_last": 371,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAPPLLLLLLASGAAACPLPCVCQNLSESLSTLCAHRGLLFVPPNVDRRTVELRLADNFI\nQALGPPDFRNMTGLVDLTLSRNAITRIGARSFGDLESLRSLHLDGNRLVELGSSSLRGPV\nNLQHLILSGNQLGRIAPGAFDDFLDSLEDLDVSYNNLRQVPWAGIGSMPALHTLNLDHNL\nIDALPPGVFAQLSQLSRLDLTSNRLATLAPDPLFSRGRDAEASPSPLVLSFSGNPLHCNC\nELLWLRRLARPDDLETCASPPTLAGRYFWAVPEGEFSCEPPLIARHTQRLWVLEGQRATL\nRCRALGDPVPTMHWVGPDDRLVGNSSRAWAFPNGTLEIGVTGAGDAGAYTCIATNPAGEA\nTARVELRVLALPHGGNTSAEGGRPGPSDIAASARTAAEGEGTLESEPAVQVTEVTATSGL\nVSWGLGRPADPVWMFQIQYNSSEDETLIYRIVPASSHHFLLKHLVPGADYDLCLLALSPA\nAGPSDLTATRLLGCAHFSTLPATPLCHALQAHVLGGTLTVAVGGVLVAALLVFTVALLVR\nGRGAGNGRLPLKLSHVQSQTNGGTSPMPKSHPPRSPPPRPQRSCSLDLGDTGGCYGYARR\nLGGAWARRSHSVHGGLLGAGCRGVGGSAERLEESVV",
"mw": 39.603,
"total_mw": 79.206,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris HCl, 100 mM NaCl, 0.02% NaN3,",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Leucine-rich repeat and fibronectin type-III domain-containing protein 4: Fragment SALM3 LRR-Ig",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "VUB",
"address": "Pleinlaan 2 1050 Brussel ",
"full_name": "Vrije Universiteit Brussel",
"webpage": "http://www.vub.ac.be/"
}
],
"contributor_name": "Alexander",
"contributor_surname": "Shkumatov",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-07-13",
"storage_temperature": 4.7,
"cell_temperature": 4.7,
"exposure_time": 1.0,
"number_of_frames": 1,
"wavelength": 0.09919,
"sample_detector_distance": 2.867,
"concentration_min": null,
"concentration_max": 12.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.154,
"s_max": 3.504,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit1_model1.pdb",
"model_mw": 99.99,
"bead_radius": 3.5,
"log": "https://www.sasbdb.org/media/log_files/refine_XMXw8QE.log",
"symmetry": "P1",
"comment": "refinement of averaged (damstart.pdb) model",
"user": 104
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDY2_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.988,
"p_value": 0.180658,
"fit_residual_plot": "SASDDY2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDY2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_jFOJhlI.log",
"software_version": "r9684",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit2_model1.pdb",
"model_mw": 86.11,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit2_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit2_model2.pdb",
"model_mw": 86.11,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit2_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit2_model3.pdb",
"model_mw": 86.11,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit2_model4_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit2_model4.pdb",
"model_mw": 86.11,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit2_model5_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
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"type_of_model": "atomic",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit2_model5.pdb",
"model_mw": 86.11,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDY2_fit2_model6_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "r9684",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDY2_fit2_model6.pdb",
"model_mw": 86.11,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDY2_fit2_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.153,
"p_value": 0.041917,
"fit_residual_plot": "SASDDY2_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDY2_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_003_1.log",
"software_version": "r9684",
"description": null
}
],
"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 Leucine-rich repeat and fibronectin type-III domain-containing protein 4 (fragment SALM3 LRR-Ig) in 20 mM Tris HCl, 100 mM NaCl, 0.02% NaN3, pH 7.5, were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). A solute concentration of 12.00 mg/ml was injected onto a size exclusion chromatography column and the eluted sample and buffer were measured at 4.7°C. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted to produce the SAXS data displayed in this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 113.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 101.4,
"porod_mw_error": null,
"pddf_i0": 17.56,
"pddf_i0_error": 0.1,
"guinier_i0": 17.51,
"guinier_i0_error": 0.04,
"pddf_rg": 3.753,
"pddf_rg_error": 0.01,
"guinier_rg": 3.74,
"guinier_rg_error": 0.01,
"pddf_dmax": 12.13,
"pddf_dmax_error": 1.0,
"porod_volume": 182.6,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 13,
"guinier_point_last": 42,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDY2_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:45.283215+02:00",
"bragg_peak": []
}
