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": "SASDD23",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"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/SASDD23.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD23.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD23_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD23_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD23_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD23_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD23.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": "1 x 5 mm",
"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 5",
"short_name": "LRR-Ig-FN",
"sequence": "QICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRLADNFVTNIKRKDFANMTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITNDMFSGLSNLHHLILNNNQLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLHTLSLDHNMIDNIPKGTFSHLHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPSTFALSFGGNPLHCNCELLWLRRLSRE\r\nDDLETCASPALLTGRYFWSIPEEEFLCEPPLITRHTHEMRVLEGQRATLRCKARGDPEPAIHWISPEGKLISNATRSLVY\r\nDNGTLDILITTVKDTGAFTCIASNPAGEATQTVDLHIIKGSEVLFQ",
"organism": "Mus musculus",
"uniprot_code": "Q8BXA0",
"uniprot_range_first": 18,
"uniprot_range_last": 376,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MEKFLFYLFLIGIAVRAQICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRLAD\nNFVTNIKRKDFANMTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITNDMFS\nGLSNLHHLILNNNQLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLHTLSLDH\nNMIDNIPKGTFSHLHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPSTFALSFGGN\nPLHCNCELLWLRRLSREDDLETCASPALLTGRYFWSIPEEEFLCEPPLITRHTHEMRVLE\nGQRATLRCKARGDPEPAIHWISPEGKLISNATRSLVYDNGTLDILITTVKDTGAFTCIAS\nNPAGEATQTVDLHIIKLPHLLNSTNHIHEPDPGSSDISTSTKSGSNASSSNGDTKMSQDK\nIVVAEATSSTALLKFNFQRNIPGIRMFQIQYNGTYDDTLVYRMIPPTSKTFLVNNLASGT\nMYDLCVLAIYDDGITSLTATRVVGCIQFTTEQDYVRCHFMQSQFLGGTMIIIIGGIIVAS\nVLVFIIILMIRYKVCNNNGQHKVTKVSNVYSQTNGAQMQGCSVTLPQSMSKQAMGHEENA\nQCCKVASDNAIQSSETCSSQDSSTTTSALPPTWTSSAPVSQKQKRKTGTKPSAEPQSEAV\nTNVESQNTNRNNSTALQLASCPPDSVTEGPTSQRAHTKPNALLTNVDQNVQETQRLESI",
"mw": 41.018,
"total_mw": 82.036,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "30 mM Tris-Cl, 150 mM NaCl, 3% glycerol",
"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 5: Fragment SALM5 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": "2016-06-08",
"storage_temperature": 15.0,
"cell_temperature": 15.0,
"exposure_time": 10.0,
"number_of_frames": 18,
"wavelength": 0.1005,
"sample_detector_distance": 4.036,
"concentration_min": 1.0,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.222,
"s_max": 3.501,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_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/SASDD23_fit1_model1.pdb",
"model_mw": 90.355,
"bead_radius": 3.25,
"log": "https://www.sasbdb.org/media/log_files/refine_QIuM8uc.log",
"symmetry": "P1",
"comment": "averaged (damstart.pdb) refined model",
"user": 104
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD23_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.29,
"p_value": 0.0,
"fit_residual_plot": "SASDD23_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD23_fit1.fir",
"fit_log": null,
"software_version": "r9684",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_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/SASDD23_fit2_model1.pdb",
"model_mw": 87.21,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_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/SASDD23_fit2_model2.pdb",
"model_mw": 87.21,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_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/SASDD23_fit2_model3.pdb",
"model_mw": 87.21,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_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/SASDD23_fit2_model4.pdb",
"model_mw": 87.21,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit2_model5_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/SASDD23_fit2_model5.pdb",
"model_mw": 87.21,
"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/SASDD23_fit2_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.226,
"p_value": 0.0,
"fit_residual_plot": "SASDD23_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD23_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_005_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 5 (fragment SALM5 (LRR-Ig)) in 30 mM Tris-Cl, 150 mM NaCl, 3% v/v glycerol, pH 7.5, were collected on the B21 beam line at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1005 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 5 mg/ml were measured at 15°C. 18 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 101.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 91.1,
"porod_mw_error": null,
"pddf_i0": 0.00669,
"pddf_i0_error": 0.0001,
"guinier_i0": 0.006724,
"guinier_i0_error": 3e-05,
"pddf_rg": 3.65,
"pddf_rg_error": 0.01,
"guinier_rg": 3.63,
"guinier_rg_error": 0.02,
"pddf_dmax": 13.5,
"pddf_dmax_error": 1.0,
"porod_volume": 155.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 50,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD23_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:46.196867+02:00",
"bragg_peak": []
}
