The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
full_entry_zip：source record and ZIP contents (10 items)
{
"path": "/data/saxsdb/sasbdb/entries/r4/sasdbr4/source/SASDBR4.zip",
"role": "full_entry_zip",
"sha256": "50797adeb67f151b936e7ca5ba24c60f6f9c8064c15c3ae7594184875c69ee02",
"size": 83975,
"status": "downloaded",
"url": "https://www.sasbdb.org/media/zip_directories/SASDBR4.zip",
"zip_member_count": 10,
"zip_members": [
{
"crc32": "5c9f912a",
"name": "SASDBR4/experimental_data/SASDBR4.dat",
"size": 11211
},
{
"crc32": "d66ed498",
"name": "SASDBR4/pddf/SASDBR4.out",
"size": 24007
},
{
"crc32": "97ab6690",
"name": "SASDBR4/SASDBR4_fit1.fit",
"size": 12331
},
{
"crc32": "d54ce9fc",
"name": "SASDBR4/SASDBR4_fit1_model1.pdb",
"size": 177390
},
{
"crc32": "6c6f5e16",
"name": "SASDBR4/SASDBR4_fit1_rg_distribution.dat",
"size": 2557
},
{
"crc32": "364703f2",
"name": "SASDBR4/SASDBR4_fit2.fir",
"size": 13481
},
{
"crc32": "04739a40",
"name": "SASDBR4/SASDBR4_fit2_model1.pdb",
"size": 51496
},
{
"crc32": "e05e612c",
"name": "SASDBR4/additional_files/Hsp90 ATPase_1_EOM_results.zip",
"size": 15908
},
{
"crc32": "ebefb09e",
"name": "SASDBR4/additional_files/LbAha1SAXScurve.dat",
"size": 12623
},
{
"crc32": "f615affe",
"name": "SASDBR4/additional_files/README.txt",
"size": 248
}
],
"zip_validation": "central_directory_readable"
}Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDBR4",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Low resolution structural studies indicate that the activator of Hsp90 ATPase 1 (Aha1) of Leishmania braziliensis has an elongated shape which allows its interaction with both N- and M-domains of Hsp90.",
"publication": {
"title": "Low resolution structural studies indicate that the activator of Hsp90 ATPase 1 (Aha1) of Leishmania braziliensis has an elongated shape which allows its interaction with both N- and M-domains of Hsp90.",
"author_list": "Seraphim TV, Alves MM, Silva IM, Gomes FE, Silva KP, Murta SM, Barbosa LR, Borges JC",
"journal": "PLoS One",
"doi": "10.1371/journal.pone.0066822",
"pmid": "23826147",
"published_date": "2013"
},
"status": "released",
"submitted_date": "2016-04-07",
"released_date": "2016-09-01"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBR4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBR4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBR4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBR4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBR4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "MAR 165 CCD",
"resolution": null
},
"name": "Brazilian Synchrotron Light Laboratory",
"city": "Campinas",
"country": "Brazil",
"beamline_name": "SAXS2 Beamline",
"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": "Activator of Hsp90 ATPase-1",
"short_name": "LbAha1",
"sequence": "MAKVGEGDPRWIVSERTDGANVNSWHWEERDLSQHTHDKLKSVFAEHAIPVPADMATSVEYLKIEEVSEI\r\nSGDVTVAQRKGKMMCYFELKMSLRWVGKMSGADQVIRGKMEVAEVDHDGFKDEYDIAVTCQENDSAAQLL\r\nESVVQVAGRSTVRQGIATFFDALFAEYHIGKQLKSGAALPPPPPPLSASASTTLATNAAAGKKSVTPSKS\r\nSSGSGDENTSFSWKMRWGAPVAELYAAMTDPSRVSVYTRSPASMDVKAGGLFSFLGGVISGYYVDVQPST\r\nLIRQQWRLSSWPVGVHSSVVLQLVKEEPGVTTLEFTQSGIPAGQLQSVQEGWKANFFEAIKVVFGYSLEY\r\nI",
"organism": "Leishmania braziliensis",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 38.254,
"total_mw": 38.254,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM Sodium phosphate, 50 mM NaCl, 2 mM EDTA, 1 mM β-mercaptoethanol",
"concentration_unit": null,
"comment": null,
"additive": "50 mM NaCl, 2 mM EDTA, 1 mM β-mercaptoethanol",
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Leishmania braziliensis Activator of Hsp90 ATPase-1 (LbAha1) ",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "São Carlos - SP - Brasil",
"full_name": "Instituto de Química de São Carlos",
"webpage": ""
}
],
"contributor_name": "Júlio",
"contributor_surname": "Borges",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2013-06-01",
"storage_temperature": null,
"cell_temperature": null,
"exposure_time": 300.0,
"number_of_frames": 3,
"wavelength": null,
"sample_detector_distance": null,
"concentration_min": 1.1,
"concentration_max": 3.2,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.177,
"s_max": 3.517,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR4_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/SASDBR4_fit1_model1.pdb",
"model_mw": 38.82,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 100
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBR4_fit1_fixed_fit_img.png",
"software": null,
"chi_square_value": 3.86,
"p_value": 0.2075,
"fit_residual_plot": "fit4columns445_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBR4_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBR4_fit2_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/SASDBR4_fit2_model1.pdb",
"model_mw": 38.995,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 100
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBR4_fit2_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.57,
"p_value": 0.028,
"fit_residual_plot": "SASDBR4_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBR4_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "Ab initio model of Leishmania braziliensis Activator of Hsp90 ATPase-1 (LbAha1) and Ensemble Optimization Method analysis on LbAha1 conformational dynamics. Results showed that LbAha1 is remarkably flexible.",
"experiment_description": "Synchrotron SAXS data from solutions of Leishmania braziliensis Activator of Hsp90 ATPase-1 in 50 mM sodium phosphate, 50 mM NaCl, 2 mM EDTA, 1 mM β-mercaptoethanol, pH 7, were collected on the SAXS2 Beamline camera on the storage ring Brazilian Synchrotron Light Laboratory (Campinas, Brazil) using a MAR Image Plate detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.1488 nm). Different solute concentrations in the range 1.10-3.20 mg/ml were measured. Three successive 300 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 different curves were scaled for protein concentration. The low angle data collected were merged with the highest concentration high angle data to yield the final composite scattering curve. \r\n\r\nThe Ensemble Optimization Method (EOM) model displayed in this entry is a structural representative from a final refined pool of flexible structures. Additional EOM results, including the Rg and Dmax distributions from two EOM modelling runs, are included in the full entry zip archive. ",
"tags": [],
"intensity_unit": null,
"experimental_mw": 47.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.03091,
"pddf_i0_error": null,
"guinier_i0": 0.03,
"guinier_i0_error": null,
"pddf_rg": 3.88,
"pddf_rg_error": null,
"guinier_rg": 3.56,
"guinier_rg_error": null,
"pddf_dmax": 14.5,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 3,
"guinier_point_last": 14,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBR4_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:27:58.948855+02:00",
"bragg_peak": []
}
