full_entry_zip:来源记录与 ZIP 内部目录(15 项)
{
"path": "/data/saxsdb/sasbdb/entries/w6/sasdbw6/source/SASDBW6.zip",
"role": "full_entry_zip",
"sha256": "07d720dbd72785c7208c6c5f89cbec32d2928a7867a812c8568d74cfdb2ca7f2",
"size": 423570,
"status": "downloaded",
"url": "https://www.sasbdb.org/media/zip_directories/SASDBW6.zip",
"zip_member_count": 15,
"zip_members": [
{
"crc32": "7b1e04b5",
"name": "SASDBW6/experimental_data/SASDBW6.dat",
"size": 8172
},
{
"crc32": "0ae76788",
"name": "SASDBW6/pddf/SASDBW6.out",
"size": 17602
},
{
"crc32": "96dbb73a",
"name": "SASDBW6/SASDBW6_fit1.fit",
"size": 11178
},
{
"crc32": "c7bd5996",
"name": "SASDBW6/SASDBW6_fit1_model1.pdb",
"size": 342479
},
{
"crc32": "64b8e911",
"name": "SASDBW6/SASDBW6_fit2.fit",
"size": 8823
},
{
"crc32": "fb6dcee5",
"name": "SASDBW6/SASDBW6_fit2_model1.pdb",
"size": 278025
},
{
"crc32": "44f6aba8",
"name": "SASDBW6/SASDBW6_fit2_model2.pdb",
"size": 278025
},
{
"crc32": "2c222bad",
"name": "SASDBW6/SASDBW6_fit2_model3.pdb",
"size": 278025
},
{
"crc32": "6f506289",
"name": "SASDBW6/SASDBW6_fit2_model4.pdb",
"size": 278025
},
{
"crc32": "c91d0002",
"name": "SASDBW6/SASDBW6_fit2_rg_distribution.dat",
"size": 2383
},
{
"crc32": "4058c73a",
"name": "SASDBW6/additional_files/SASDBW6_CORAL_run11.log",
"size": 14515
},
{
"crc32": "42c26dcd",
"name": "SASDBW6/additional_files/SASDBW6_EOM_logFile_003_1.log",
"size": 3033
},
{
"crc32": "c91d0002",
"name": "SASDBW6/additional_files/SASDBW6_Rg_distr_003_1.dat",
"size": 2383
},
{
"crc32": "7fdeafe3",
"name": "SASDBW6/additional_files/SASDBW6_Size_distr_003_1.dat",
"size": 2383
},
{
"crc32": "2820810c",
"name": "SASDBW6/additional_files/README.txt",
"size": 292
}
],
"zip_validation": "central_directory_readable"
}查看完整 summary.json 原文
{
"code": "SASDBW6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "A shape-shifting redox foldase contributes to Proteus mirabilis copper resistance.",
"publication": {
"title": "A shape-shifting redox foldase contributes to Proteus mirabilis copper resistance.",
"author_list": "Furlong EJ, Lo AW, Kurth F, Premkumar L, Totsika M, Achard MES, Halili MA, Heras B, Whitten AE, Choudhury HG, Schembri MA, Martin JL",
"journal": "Nat Commun",
"doi": "10.1038/ncomms16065",
"pmid": "28722010",
"published_date": "2017 Jul 19"
},
"status": "released",
"submitted_date": "2016-10-04",
"released_date": "2017-06-16"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBW6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBW6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBW6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBW6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBW6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBW6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBW6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Australian Synchrotron",
"city": "Melbourne",
"country": "Australia",
"beamline_name": "SAXS/WAXS",
"beam_geometry": "Point",
"type_of_source": "X-ray synchrotron",
"point_source": true,
"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": "Suppressor of Copper Sensitivity C protein (mutant)",
"short_name": "PmScsC (DsbA-like)",
"sequence": "AALNAAQEKEVRALVRDTLVSNPEILEEAIMALQTKAEAAAKEAAAKAALASEHDALYNDAASPRIGAKDAKLVLVSFTDYNCPYCKRFDPLLEKITEQYPDVAVIIKPLPFKGESSAKASQAVLSVWKEDPKAFLALHQRLMQKKTMLDNASIEDAMKSTNTSKIKLTDDSLKTLQNNLELSRKLGIQGTPATVIGDTILPGAVDYDQLEIIVKEQLAKVKK",
"organism": "Proteus mirabilis",
"uniprot_code": "C2LPE2",
"uniprot_range_first": 22,
"uniprot_range_last": 243,
"oligomerization": "trimer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 24.32,
"total_mw": 72.96,
"number_molecules": 3,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM HEPES 150mM NaCl, 1mM DTT,",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Suppressor of Copper Sensitivity C protein (ScsC) from P. mirabilis (mutant)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "ANSTO",
"address": "Kirrawee DC, NSW 2232, Australia",
"full_name": "Australian Nuclear Science and Technology Organisation",
"webpage": ""
}
],
"contributor_name": "Andrew",
"contributor_surname": "Whitten",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-07-22",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 23.0,
"number_of_frames": 23,
"wavelength": 0.1033,
"sample_detector_distance": 1.485,
"concentration_min": 0.6,
"concentration_max": 5.3,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.106,
"s_max": 2.499,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBW6_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "4xvw",
"ext_code": "4XVW",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "05",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBW6_fit1_model1.pdb",
"model_mw": 73.15,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/run11_c7f8qut.log",
"symmetry": "C3",
"comment": "",
"user": 111
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBW6_fit1_fixed_fit_img.png",
"software": null,
"chi_square_value": 4.85,
"p_value": 0.0,
"fit_residual_plot": "SASDBW6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBW6_fit1.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBW6_fit2_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/SASDBW6_fit2_model1.pdb",
"model_mw": 73.7,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/EOM_logFile_003_1.log",
"symmetry": "C3",
"comment": "",
"user": 111
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBW6_fit2_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/SASDBW6_fit2_model2.pdb",
"model_mw": 73.7,
"bead_radius": 1.9,
"log": null,
"symmetry": "C3",
"comment": "",
"user": 111
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBW6_fit2_model3_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/SASDBW6_fit2_model3.pdb",
"model_mw": 73.7,
"bead_radius": 1.9,
"log": null,
"symmetry": "C3",
"comment": "",
"user": 111
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBW6_fit2_model4_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/SASDBW6_fit2_model4.pdb",
"model_mw": 73.7,
"bead_radius": 1.9,
"log": null,
"symmetry": "C3",
"comment": "",
"user": 111
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBW6_fit2_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.87,
"p_value": 0.045,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBW6_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM v4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "X-ray synchrotron radiation scattering data from solutions of a Suppressor of Copper Sensitivity C mutant protein (ScsC) from P. mirabilis in 25 mM HEPES 150mM NaCl, 1mM DTT, pH 7.5 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). Twenty three successive 1 second frames were collected across solute concentrations of 0.60-5.30 mg/ml. The SAXS data displayed this entry was derived from a 1.30 mg/ml sample. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from rigid-body modelling using CORAL (top) and a representative ensemble of four trimeric ScsC structures determined using ensemble optimization method (EOM). The Rg and Dmax distributions derived from EOM are included in the full entry zip archive.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 76.4,
"experimental_mw_error": null,
"guinier_i0_mw": 76.4,
"guinier_i0_mw_error": 3.5,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.06648,
"pddf_i0_error": 7e-05,
"guinier_i0": 0.0663,
"guinier_i0_error": 0.0001,
"pddf_rg": 4.41,
"pddf_rg_error": 0.01,
"guinier_rg": 4.38,
"guinier_rg_error": 0.02,
"pddf_dmax": 13.5,
"pddf_dmax_error": 0.7,
"porod_volume": 108.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 14,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBW6_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:28:08.238471+02:00",
"bragg_peak": []
}