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": "SASDCM6",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.",
"publication": {
"title": "Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.",
"author_list": "Shin D, Na W, Lee JH, Kim G, Baek J, Park SH, Choi CY, Lee S",
"journal": "Elife",
"doi": "10.7554/eLife.29154",
"pmid": "28968219",
"published_date": "2017 Oct 2"
},
"status": "released",
"submitted_date": "2017-07-18",
"released_date": "2018-03-19"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCM6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCM6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCM6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCM6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "CCD",
"name": "ADSC Quantum 315",
"resolution": 315.0
},
"name": "Pohang Accelerator Laboratory",
"city": "Pohang",
"country": "South Korea",
"beamline_name": "4C",
"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": "Monoubiquitinated Rab5 at K165",
"short_name": "mUbRab5K165",
"sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN\r\nIQKESTLHLVLRLRGG\r\nMASRGATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQ\r\nTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQR\r\nQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKK\r\nLPKNEPQNPGANSARGRGVDLTEPTQPTRNQCCSN",
"organism": "Homo sapiens",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 32.205,
"total_mw": 32.205,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Small GTPase Rab5 conjugated with ubiquitin at K116",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Seoul, SK",
"full_name": "Sungkyunkwan University",
"webpage": "http://www.skku.edu/eng_home/index.jsp"
}
],
"contributor_name": "Donghyuk",
"contributor_surname": "Shin",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-11-21",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 10.0,
"number_of_frames": 6,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": 0.4,
"concentration_max": 2.9,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.102,
"s_max": 1.494,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCM6_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCM6_fit1_model1.pdb",
"model_mw": 27.63,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 234
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCM6_fit1_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCM6_fit1_model2.pdb",
"model_mw": 27.63,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 234
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCM6_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.2,
"p_value": 0.0138,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCM6_fit1.fit",
"fit_log": null,
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCM6_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCM6_fit2_model1.pdb",
"model_mw": 40.1,
"bead_radius": 1.8,
"log": null,
"symmetry": "",
"comment": "The lowest NSD model from damaver with 10 independent dammif runs",
"user": 234
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCM6_fit2_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.32,
"p_value": 0.0139,
"fit_residual_plot": "SASDCM6_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCM6_fit2.fir",
"fit_log": null,
"software_version": "",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 30.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 0.73,
"guinier_i0_error": 0.0045,
"pddf_rg": 2.653,
"pddf_rg_error": null,
"guinier_rg": 2.554,
"guinier_rg_error": 0.042,
"pddf_dmax": 8.66,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": null,
"guinier_point_last": null,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCM6_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:28:06.019492+02:00",
"bragg_peak": []
}
