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": "SASDG54",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/A",
"project": {
"title": "Mannose receptor (CD206) activation in tumor-associated macrophages enhances adaptive and innate antitumor immune responses.",
"publication": {
"title": "Mannose receptor (CD206) activation in tumor-associated macrophages enhances adaptive and innate antitumor immune responses.",
"author_list": "Jaynes JM, Sable R, Ronzetti M, Bautista W, Knotts Z, Abisoye-Ogunniyan A, Li D, Calvo R, Dashnyam M, Singh A, Guerin T, White J, Ravichandran S, Kumar P, Talsania K, Chen V, Ghebremedhin A, Karanam B, Bin Salam A, Amin R, Odzorig T, Aiken T, Nguyen V, Bian Y, Zarif JC, de Groot AE, Mehta M, Fan L, Hu X, Simeonov A, Pate N, Abu-Asab M, Ferrer M, Southall N, Ock CY, Zhao Y, Lopez H, Kozlov S, de Val N, Yates CC, Baljinnyam B, Marugan J, Rudloff U",
"journal": "Sci Transl Med",
"doi": "10.1126/scitranslmed.aax6337",
"pmid": "32051227",
"published_date": "2020 Feb 12"
},
"status": "released",
"submitted_date": "2019-08-14",
"released_date": "2020-02-17"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG54.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG54.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG54_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG54_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG54_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG54_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG54.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Advanced Photon Source (APS), Argonne National Laboratory",
"city": "Lemont, IL",
"country": "USA",
"beamline_name": "12-ID-B SAXS/WAXS",
"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": "Macrophage mannose receptor 1",
"short_name": "MRC1 or CD206",
"sequence": "LLDTRQFLIYNEDHKRCVDAVSPSAVQTAACNQDAESQKFRWVSESQIMSVAFKLCLGVPSKTDWVAITLYACDSKSEFQKWECKNDTLLGIKGEDLFFNYGNRQEKNIMLYKGSGLWSRWKIYGTTDNLCSRGYEAMYTLLGNANGATCAFPFKFENKWYADCTSAGRSDGWLWCGTTTDYDTDKLFGYCPLKFEGSESLWNKDPLTSVSYQINSKSALTWHQARKSCQQQNAELLSITEIHEQTYLTGLTSSLTSGLWIGLNSLSFNSGWQWSDRSPFRYLNWLPGSPSAEPGKSCVSLNPGKNAKWENLECVQKLGYICKKGNTTLNSFVIPSESDVPTHCPSQWWPYAGHCYKIHRDEKKIQRDALTTCRKEGGDLASIHTIEEYDFIISQLGYEPNDELWIGLNDIKIQMYFEWSDGTPVTFTKWLRGEPSHENNRQEDCVVMKGKDGYWADRGCEWPLGYICKMKSRSQGPEIVEVEKGCRKGWKKHHFYCYMIGHTLSTFAEANQTCNNENAYLTTIEDRYEQAFLTSFVGLRPEKYFWTGLSDIQTKGTFQWTIEEEVRFTHWNSDMPGRKPGCVAMRTGIAGGLWDVLKCDEKAKFVCKHWAEGVTHPPKPTTTPEPKCPEDWGASSRTSLCFKLYAKGKHEKKTWFESRDFCRALGGDLASINNKEEQQTIWRLITASGSYHKLFWLGLTYGSPSEGFTWSDGSPVSYENWAYGEPNNYQNVEYCGELKGDPTMSWNDINCEHLNNWICQIQKGQTPKPEPTPAPQDNPPVTEDGWVIYKDYQYYFSKEKETMDNARAFCKRNFGDLVSIQSESEKKFLWKYVNRNDAQSAYFIGLLISLDKKFAWMDGSKVDYVSWATGEPNFANEDENCVTMYSNSGFWNDINCGYPNAFICQRHNSSINATTVMPTMPSVPSGCKEGWNFYSNKCFKIFGFMEEERKNWQEARKACIGFGGNLVSIQNEKEQAFLTYHMKDSTFSAWTGLNDVNSEHTFLWTDGRGVHYTNWGKGYPGGRRSSLSYEDADCVVIIGGASNEAGKWMDDTCDSKRGYICQTRSDPSLTNPPATIQTDGFVKYGKSSYSLMRQKFQWHEAETYCKLHNSLIASILDPYSNAFAWLQMETSNERVWIALNSNLTDNQYTWTDKWRVRYTNWAADEPKLKSACVYLDLDGYWKTAHCNESFYFLCKRSDEIPATEPPQLPGRCPESDHTAWIPFHGHCYYIESSYTRNWGQASLECLRMGSSLVSIESAAESSFLSYRVEPLKSKTNFWIGLFRNVEGTWLWINNSPVSFVNWNTGDPSGERNDCVALHASSGFWSNIHCSSYKGYICKRPKIIDAKPTHELLTTKADTRKMDPSKPSSNVHHHHHH",
"organism": "Mouse myeloma cell line",
"uniprot_code": "P22897",
"uniprot_range_first": 19,
"uniprot_range_last": 1388,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MRLPLLLVFASVIPGAVLLLDTRQFLIYNEDHKRCVDAVSPSAVQTAACNQDAESQKFRW\nVSESQIMSVAFKLCLGVPSKTDWVAITLYACDSKSEFQKWECKNDTLLGIKGEDLFFNYG\nNRQEKNIMLYKGSGLWSRWKIYGTTDNLCSRGYEAMYTLLGNANGATCAFPFKFENKWYA\nDCTSAGRSDGWLWCGTTTDYDTDKLFGYCPLKFEGSESLWNKDPLTSVSYQINSKSALTW\nHQARKSCQQQNAELLSITEIHEQTYLTGLTSSLTSGLWIGLNSLSFNSGWQWSDRSPFRY\nLNWLPGSPSAEPGKSCVSLNPGKNAKWENLECVQKLGYICKKGNTTLNSFVIPSESDVPT\nHCPSQWWPYAGHCYKIHRDEKKIQRDALTTCRKEGGDLTSIHTIEELDFIISQLGYEPND\nELWIGLNDIKIQMYFEWSDGTPVTFTKWLRGEPSHENNRQEDCVVMKGKDGYWADRGCEW\nPLGYICKMKSRSQGPEIVEVEKGCRKGWKKHHFYCYMIGHTLSTFAEANQTCNNENAYLT\nTIEDRYEQAFLTSFVGLRPEKYFWTGLSDIQTKGTFQWTIEEEVRFTHWNSDMPGRKPGC\nVAMRTGIAGGLWDVLKCDEKAKFVCKHWAEGVTHPPKPTTTPEPKCPEDWGASSRTSLCF\nKLYAKGKHEKKTWFESRDFCRALGGDLASINNKEEQQTIWRLITASGSYHKLFWLGLTYG\nSPSEGFTWSDGSPVSYENWAYGEPNNYQNVEYCGELKGDPTMSWNDINCEHLNNWICQIQ\nKGQTPKPEPTPAPQDNPPVTEDGWVIYKDYQYYFSKEKETMDNARAFCKRNFGDLVSIQS\nESEKKFLWKYVNRNDAQSAYFIGLLISLDKKFAWMDGSKVDYVSWATGEPNFANEDENCV\nTMYSNSGFWNDINCGYPNAFICQRHNSSINATTVMPTMPSVPSGCKEGWNFYSNKCFKIF\nGFMEEERKNWQEARKACIGFGGNLVSIQNEKEQAFLTYHMKDSTFSAWTGLNDVNSEHTF\nLWTDGRGVHYTNWGKGYPGGRRSSLSYEDADCVVIIGGASNEAGKWMDDTCDSKRGYICQ\nTRSDPSLTNPPATIQTDGFVKYGKSSYSLMRQKFQWHEAETYCKLHNSLIASILDPYSNA\nFAWLQMETSNERVWIALNSNLTDNQYTWTDKWRVRYTNWAADEPKLKSACVYLDLDGYWK\nTAHCNESFYFLCKRSDEIPATEPPQLPGRCPESDHTAWIPFHGHCYYIESSYTRNWGQAS\nLECLRMGSSLVSIESAAESSFLSYRVEPLKSKTNFWIGLFRNVEGTWLWINNSPVSFVNW\nNTGDPSGERNDCVALHASSGFWSNIHCSSYKGYICKRPKIIDAKPTHELLTTKADTRKMD\nPSKPSSNVAGVVIIVILLILTGAGLAAYFFYKKRRVHLPQEGAFENTLYFNSQSSPGTSD\nMKDLVGNIEQNEHSVI",
"mw": 157.497,
"total_mw": 314.994,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50mM Hepes, 100mM NaCl, 1mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Human macrophage mannose receptor 1 protein",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "NIH",
"address": "Bethesda, Maryland, USA",
"full_name": "National Institutes of Health, Bethesda, MD",
"webpage": "https://www.nih.gov/"
}
],
"contributor_name": "Liz",
"contributor_surname": "Fan",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-04-15",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 30,
"wavelength": 0.093,
"sample_detector_distance": 2.0,
"concentration_min": 0.88,
"concentration_max": 1.76,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.045,
"s_max": 10.4,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG54_fit1_model1_img.png",
"software": "iTASSER",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDG54_fit1_model1.pdb",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Giving silicon model is for MRC1/CD206 monomer.",
"user": 481
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG54_fit1_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.94,
"p_value": 0.0,
"fit_residual_plot": "SASDG54_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG54_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/q06red1l.log",
"software_version": null,
"description": "Two monomer PDB files were used for the fitting to scattering profiles from a dimer."
}
],
"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 human macrophage mannose receptor 1 in 50 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7 were collected on the 12ID-B SAXS/WAXS beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Pilatus 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.093 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.9 and 1.8 mg/ml were measured at 20°C. 30 successive 1 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 concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 345.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 345.0,
"porod_mw_error": null,
"pddf_i0": 0.5277,
"pddf_i0_error": null,
"guinier_i0": 0.53,
"guinier_i0_error": 0.01,
"pddf_rg": 8.23,
"pddf_rg_error": 0.2,
"guinier_rg": 7.89,
"guinier_rg_error": 0.8,
"pddf_dmax": 30.1,
"pddf_dmax_error": null,
"porod_volume": 584.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 9,
"guinier_point_last": 63,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDG54_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-03-02T16:54:16.648202+01:00",
"bragg_peak": []
}
