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": "SASDC22",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans.",
"publication": {
"title": "Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans.",
"author_list": "Bhati M, Llamosas E, Jacques DA, Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM",
"journal": "Sci Rep",
"doi": "10.1038/s41598-017-04587-8",
"pmid": "28676648",
"published_date": "2017 Jul 4"
},
"status": "released",
"submitted_date": null,
"released_date": "2017-07-08"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC22.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC22.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC22_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC22_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC22_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC22_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC22.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "KAF 2084 x 2084 SCX CCD",
"name": "Roper Scientific PI-SCX:4300",
"resolution": 24.0
},
"name": "University of Sydney",
"city": "Sydney",
"country": "Australia",
"beamline_name": "Anton Paar SAXSess",
"beam_geometry": "Line collimation",
"type_of_source": "X-ray in house",
"point_source": false,
"line_collimation": true,
"sample_path_length": 1.0,
"line_collimation_slitlength": 10.0,
"line_collimation_integrationwidth": 10.0,
"xray_energy": null,
"beam_profile_ah": 2.8,
"beam_profile_al": 1.3
},
"sample": {
"molecule": [
{
"long_name": "Homeobox protein CEH-14",
"short_name": "CEH-14",
"sequence": "GSNNEEAICSLCDKKIRDRFVSKVNGRCYHSSCLRCSTCKDELGATCFLREDSMYCRAHF \r\nYKKFGTKCSSCNEGIVPDHVVRKASNHVYHVECFQCFICKRSLETGEEFYLIADDARLVC \r\nKDDYEQARDGGSGGHMGSGG",
"organism": "Caenorhabditis elegans",
"uniprot_code": "P20271",
"uniprot_range_first": 42,
"uniprot_range_last": 168,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MLGHNILTLGECDELDNHIVMCSTGLLSPQEDFSNVNAGHPNNEEAICSLCDKKIRDRFV\nSKVNGRCYHSSCLRCSTCKDELGATCFLREDSMYCRAHFYKKFGTKCSSCNEGIVPDHVV\nRKASNHVYHVECFQCFICKRSLETGEEFYLIADDARLVCKDDYEQARDKHCNELEGDGSN\nKRPRTTISAKSLETLKQAYQTSSKPARHVREQLASETGLDMRVVQVWFQNRRAKEKRLKK\nDAGRRWKSSNRAESDSNSPIESINGQSPNYLYLDHPMDDGNESNYLFHSREQTPDKYYRN\nETPSTDPPPMHMTTPSVLTTNFSTPLSLSTNVYNLPPPESQLIPHMTPQYI",
"mw": 15.693,
"total_mw": 15.693,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "CeLIM-7",
"short_name": "CeLIM-7",
"sequence": "GIGPLMVQPATPHIDNTLGGPIDIQHFAQWEF",
"organism": "Caenorhabditis elegans",
"uniprot_code": "G5EC36",
"uniprot_range_first": 347,
"uniprot_range_last": 376,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MNICMRNGYEQFSLTSPGTSDLEIGGSFWKDEPDTKYLCLDSPVEQRQHQPPMAVCAGCR\nLEISDRYFLRVNPNLEFHAQCLKCVQCSRPLDENQTAFVKNGQTYCRDDYRRLFTTRCSR\nCHGDFDKTDLVMRAGPQNVFHLNCFACVACEKRLQTGEEFQIKNNSLYCRSDCRGLDNPD\nTSASVPDYSKLNNNNNNDNNNSSSNFDEDEWDEERSTLTSLDNNTSSPLGSPKSDGVRTP\nLFGHHNSGSGGSTSSCGKKKKDKQATRVRTVLNENQLKILRDCYSINSRPDATLKERLVE\nMTGLSARVIRVWFQNKRCKDKKRQIQITENRLNSEREEVLNRVRVNGIGPLMVQPATPHI\nDNTLGGPIDIQHFAQWNGTPPPPPPQYGNPMMFNSPSTFDVSVILAPVAPNVTSPSEALG\nPLGASVFPHFSPQHAPFTATSHDISSPAPCGE",
"mw": 3.501,
"total_mw": 3.501,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris, 100 mM NaCl, 5 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2009-04-07",
"storage_temperature": null,
"cell_temperature": 10.0,
"exposure_time": 900.0,
"number_of_frames": 4,
"wavelength": 0.1542,
"sample_detector_distance": 0.309,
"concentration_min": null,
"concentration_max": 5.2,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.067,
"s_max": 3.311,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit1_model1.pdb",
"model_mw": 17.376,
"bead_radius": 2.25,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit1_model2_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit1_model2.pdb",
"model_mw": 17.473,
"bead_radius": 2.25,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC22_fit1_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.288,
"p_value": 0.1902,
"fit_residual_plot": "SASDC22_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC22_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_hdm80LL.log",
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit2_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC22_fit2_fit_img.png",
"software": "GASBOR",
"chi_square_value": 0.29,
"p_value": 0.0257,
"fit_residual_plot": "SASDC22_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC22_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Ceh5.log",
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit3_model1_img.png",
"software": "SwissModel",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit3_model1.pdb",
"model_mw": 18.77,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC22_fit3_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.3,
"p_value": 0.192,
"fit_residual_plot": "SASDC22_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC22_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/model_ceh14_lim7r_Znr00.log",
"software_version": "",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM5 (r8972)",
"i0_calibration_standard": null,
"description": "The SAXS data displayed for this entry includes the beam-geometry corrected scattering profile (desmeared data, top, and homology model fit) as well as the fit of the ab initio models to the smeared SAXS data (i.e., smeared model-data fits). The original smeared data, prepared experimental beam profile and all individual DAMMIF and Gasbor models are included in the full entry zip archive.",
"experiment_description": "SAXS data from solutions of the tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7 in 50 mM Tris, 100 mM NaCl, 5 mM TCEP, pH 8 were collected on an Anton Paar SAXSess 10 mm line collimated instrument (The University of Sydney, Australia) using a CCD Roper Scientific KAF 2084 x 2084 SCX CCD camera at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.1542 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 5.50 mg/ml was measured at 10°C. Four successive 900 second frames were collected. The data were normalized to the intensity of the transmitted beam and underwent 10 mm horizontal-width integration; the scattering of the solvent-blank was subtracted to produce the smeared scattering profile of the protein in solution.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 17.0,
"experimental_mw_error": null,
"guinier_i0_mw": 16.7,
"guinier_i0_mw_error": 0.9,
"porod_mw": 16.0,
"porod_mw_error": null,
"pddf_i0": 0.0833,
"pddf_i0_error": 0.002,
"guinier_i0": 0.083,
"guinier_i0_error": 0.0002,
"pddf_rg": 2.51,
"pddf_rg_error": 0.09,
"guinier_rg": 2.4,
"guinier_rg_error": 0.03,
"pddf_dmax": 8.9,
"pddf_dmax_error": null,
"porod_volume": 25.6,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 61,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDC22_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-01-10T16:55:24.317339+01:00",
"bragg_peak": []
}
