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": "SASDCJ2",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.",
"publication": {
"title": "Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.",
"author_list": "Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A",
"journal": "Biophys J",
"doi": "10.1016/j.bpj.2015.06.065",
"pmid": "26287631",
"published_date": "2015 Aug 18"
},
"status": "released",
"submitted_date": "2017-04-04",
"released_date": "2017-06-09"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCJ2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCJ2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCJ2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCJ2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Rayonix MX225-HE",
"resolution": null
},
"name": "Stanford Synchrotron Radiation Lightsource (SSRL)",
"city": "Menlo Park, CA",
"country": "USA",
"beamline_name": "BL4-2",
"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": "Major prion protein",
"short_name": "prion",
"sequence": "KKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGTWGQPHGGGWGQPHGGSWGQPHGGSWG\r\nQPHGGGWGQGGGTHNQWNKPSKPKTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPMIHFG\r\nNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETD\r\nVKMMERVVEQMCVTQYQKESQAYYDGRRS",
"organism": "Mus musculus",
"uniprot_code": "P04925",
"uniprot_range_first": 23,
"uniprot_range_last": 230,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MANLGYWLLALFVTMWTDVGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGTWGQPH\nGGGWGQPHGGSWGQPHGGSWGQPHGGGWGQGGGTHNQWNKPSKPKTNLKHVAGAAAAGAV\nVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVN\nITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYYDGRRSSSTVLFSSPP\nVILLISFLIFLIVG",
"mw": 22.932,
"total_mw": 22.932,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "P-Clone Fab, Chimera",
"short_name": "Fab-P",
"sequence": "ATQAYAELVMTQTPSSLSASLGERVSLTCRASQDIGNNLNWIQQKPDGTIKRLIYATSS\r\nLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQHDTFPLTFGGGTKLEIKRTVAAP\r\nSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY\r\nSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR\r\nAYAEVQLLEQSGAELVKPGASVKLSCTASGFNIEDSYIHWVKQRPEQGLEWIGRIDPED\r\nGETKYAPKFQGKATITADTSSNTAYLHLRRLTSEDTAIYYCGRGAYYIKEDFWGQGTTLT\r\nVSSASTKGPSVFPLAPSSKAGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS\r\nSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPA",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 47.386,
"total_mw": 47.386,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "sodium acetate buffer (20 mM sodium acetate, pH 5.1; 150 mM NaCl)",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 5.1,
"deuteration": null
},
"purity_method": null,
"name": "Solution structure of recombinant prion protein (89–230) in complex with Fab-P",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Jerusalem, Israel",
"full_name": "The Hebrew University of Jerusalem",
"webpage": "http://new.huji.ac.il"
}
],
"contributor_name": "Dina",
"contributor_surname": "Schneidman",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-12-05",
"storage_temperature": 4.0,
"cell_temperature": 9.8,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.113,
"sample_detector_distance": 1.7,
"concentration_min": 1.0,
"concentration_max": 3.7,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.124,
"s_max": 4.724,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCJ2_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "2hh0",
"ext_code": "2HH0",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCJ2_fit1_model1.pdb",
"model_mw": 69.12,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "",
"user": 206
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCJ2_fit1_model2_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCJ2_fit1_model2.pdb",
"model_mw": 69.12,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "",
"user": 206
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCJ2_fit1_fit_img.png",
"software": "FoXS",
"chi_square_value": 1.13,
"p_value": 0.058,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCJ2_fit1.fit",
"fit_log": null,
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCJ2_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCJ2_fit2_model1.pdb",
"model_mw": 69.12,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "",
"user": 206
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCJ2_fit2_fit_img.png",
"software": "FoXS",
"chi_square_value": 2.13,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCJ2_fit2.fit",
"fit_log": null,
"software_version": "",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM V5.0 (r8972)",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of recombinant prion protein (89–230) in complex with Fab-P in 20 mM sodium acetate, 150 mM NaCl, pH 5.1 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL, Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.113 nm (I(s) vs s, where s = 4πsin θ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 3.7 mg/ml were measured at 9.8°C. 10 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 and the difference curves were scaled for protein concentration. 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": null,
"experimental_mw": 73.8,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 1066.0,
"pddf_i0_error": 2.78,
"guinier_i0": 1087.12,
"guinier_i0_error": 9.23,
"pddf_rg": 3.83,
"pddf_rg_error": 0.13,
"guinier_rg": 3.92,
"guinier_rg_error": 0.02,
"pddf_dmax": 14.5,
"pddf_dmax_error": 0.5,
"porod_volume": 106.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 4,
"guinier_point_last": 15,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCJ2_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
