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": "SASDG85",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function.",
"publication": {
"title": "Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function.",
"author_list": "Seacrist CD, Kuenze G, Hoffmann RM, Moeller BE, Burke JE, Meiler J, Blind RD",
"journal": "Structure",
"doi": "10.1016/j.str.2020.04.020",
"pmid": "32433991",
"published_date": "2020 May 19"
},
"status": "released",
"submitted_date": "2019-09-11",
"released_date": "2020-04-26"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG85.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG85.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG85_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG85_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG85_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG85_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG85.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 X 2M",
"resolution": 172.0
},
"name": "Advanced Light Source (ALS)",
"city": "Berkeley, CA",
"country": "USA",
"beamline_name": "12.3.1 (SIBYLS)",
"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": "Liver Receptor Homolog-1",
"short_name": "LRH-1",
"sequence": "MAHHHHHHVDDDDKMSENLYFQSMSSNSDTGDLQESLKHGLTPIGAGLPDRHGSPIPARGRLVMLPKVETEALG\r\nLARSHGEQGQMPENMQVSQFKMVNYSYDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIEN\r\nQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKALIRANGLKLEAMSQV\r\nIQAMPSDLTISSAIQNIHSASKGLPLNHAALPPTDYDRSPFVTSPISMTMPPHGSLQGYQTYGHFPSRAIKSEY\r\nPDPYTSSPESIMGYSYMDSYQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCK\r\nMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAG\r\nATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK\r\nFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA",
"organism": "Homo sapiens",
"uniprot_code": "O00482",
"uniprot_range_first": 1,
"uniprot_range_last": 541,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSSNSDTGDLQESLKHGLTPIGAGLPDRHGSPIPARGRLVMLPKVETEALGLARSHGEQG\nQMPENMQVSQFKMVNYSYDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRY\nTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQ\nQKKALIRANGLKLEAMSQVIQAMPSDLTISSAIQNIHSASKGLPLNHAALPPTDYDRSPF\nVTSPISMTMPPHGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPAS\nIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWA\nRSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQA\nGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAA\nLLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR\nA",
"mw": 64.144,
"total_mw": 64.144,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha",
"short_name": "PGC1 alpha",
"sequence": "EEPSLLKKLLLAPA",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 1.522,
"total_mw": 1.522,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "CYP7A1 Promoter Forward",
"short_name": null,
"sequence": "GTTCAAGGCCAG",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 3.75,
"total_mw": 3.75,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "CYP7A1 Promoter Reverse",
"short_name": null,
"sequence": "CTGGCCTTGAAC",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 3.701,
"total_mw": 3.701,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM TRIS, 150 mM NaCl, 2% v/v glycerol, 0.5 mM CHAPS, 5 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Wild-type full-length Liver Receptor Homolog-1/Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha peptide complex bound to the CYP7A1 promoter oligonucleotide duplex.",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "Vanderbilt University",
"webpage": null
}
],
"contributor_name": "Corey",
"contributor_surname": "Seacrist",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2019-05-26",
"storage_temperature": null,
"cell_temperature": 20.0,
"exposure_time": 3.0,
"number_of_frames": 500,
"wavelength": 0.1127,
"sample_detector_distance": 2.105,
"concentration_min": null,
"concentration_max": 7.5,
"sample_volume": 100.0,
"flow_rate": 0.45,
"s_min": 0.153,
"s_max": 3.704,
"total_exposure_time": null,
"seccolumn": 17
},
"fits": [],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of WT flLRH-1 / CYP7A1 oligo duplex / PGC1 alpha co-activator peptide in 20 mM TRIS, 150 mM NaCl, 2% v/v glycerol, 0.5 mM CHAPS, 5 mM DTT, pH 7.5 were collected on the SIBYLS 12.3.1 beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 7.5 mg/ml was injected at a 0.45 ml/min flow rate onto a Shodex KW-800 series column at 20°C. 500 successive 3 second frames were collected continuously during the ~25 minute elution. After 2D-to-1D radial averaging, the data were analyzed through the SEC elution peak of the sample (from which I(0) and Rg were evaluated using the Guinier approximation) and the scattering of an appropriate solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 67.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 23.72,
"pddf_i0_error": null,
"guinier_i0": 23.89,
"guinier_i0_error": 0.22,
"pddf_rg": 3.907,
"pddf_rg_error": 0.02,
"guinier_rg": 3.819,
"guinier_rg_error": 0.046,
"pddf_dmax": 13.0,
"pddf_dmax_error": null,
"porod_volume": 76.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 34,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDG85_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-05-25T10:01:18.364006+02:00",
"bragg_peak": []
}
