查看完整 summary.json 原文
{
"code": "SASDDG3",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with 40 bp DNA",
"publication": null,
"status": "released",
"submitted_date": "2018-02-08",
"released_date": "2019-12-02"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDG3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDG3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDG3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDG3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDG3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDG3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDG3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"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": "Sa0446 binding sequence 40bp",
"short_name": "40bp dsDNA",
"sequence": "GTAGTAAGATTTAAAAAAACATACTAAGATATAAATTAAC\r\nGTTAATTTATATCTTAGTATGTTTTTTTAAATCTTACTAC",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 24.721,
"total_mw": 24.721,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Transcriptional regulator Lrs14-like protein",
"short_name": "AbfR2",
"sequence": "MGSSHHHHHHSQDPNSMETVLQIPYQKKTQIEKLLEFMYGLNEKEVQLIFRLLYSDTKLN \r\nIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGRKGRPIYVYYVDREQLFKRISRD \r\nLEELVQASIAKLKEYIFKS",
"organism": "Sulfolobus acidocaldarius",
"uniprot_code": "Q4J9G1",
"uniprot_range_first": 1,
"uniprot_range_last": 123,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "METVLQIPYQKKTQIEKLLEFMYGLNEKEVQLIFRLLYSDTKLNIEELAEEFKVSKALIS\nKSLSELANKGLIEREKVSNEGRKGRPIYVYYVDREQLFKRISRDLEELVQASIAKLKEYI\nFKS",
"mw": 16.368,
"total_mw": 32.736,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "300 mM NaCl, 20 mM HEPES, pH 7.5",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Marburg, Germany",
"full_name": "University of Marburg",
"webpage": "http://www.uni-marburg.de/"
}
],
"contributor_name": "Marian",
"contributor_surname": "Vogt",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-11-05",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.124,
"sample_detector_distance": null,
"concentration_min": null,
"concentration_max": 0.63,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.035,
"s_max": 4.944,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDG3_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDG3_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 2.7,
"log": "https://www.sasbdb.org/media/log_files/Dammif_P1_slow_Saci12230446p_merged029_030-10.log",
"symmetry": null,
"comment": null,
"user": 255
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDG3_fit1_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.278,
"p_value": 0.0,
"fit_residual_plot": "SASDDG3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDG3_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dammif_P1_slow_Saci12230446p_merged029_030-10.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDG3_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDG3_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 2.7,
"log": "https://www.sasbdb.org/media/log_files/Dammif_P2_slow_Saci12230446p_merged029_030-8-1.pdb",
"symmetry": null,
"comment": null,
"user": 255
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDG3_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.34,
"p_value": 1.3e-05,
"fit_residual_plot": "SASDDG3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDG3_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dammif_P2_slow_Saci12230446p_merged029_030-8.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Archaeal biofilm regulator 2 (AbfR2) in complex with 40 base-pair dsDNA (Sa0446 binding sequence) in 300 mM NaCl, 20 mM HEPES, pH 7.5, were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.63 mg/ml was measured at 4°C. 10 successive 1 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.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 41.981,
"experimental_mw_error": null,
"guinier_i0_mw": 67.74,
"guinier_i0_mw_error": 0.0,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 68.09,
"pddf_i0_error": null,
"guinier_i0": 67.74,
"guinier_i0_error": 0.17,
"pddf_rg": 3.561,
"pddf_rg_error": null,
"guinier_rg": 3.44,
"guinier_rg_error": 0.81,
"pddf_dmax": 12.8,
"pddf_dmax_error": null,
"porod_volume": 60.38,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 18,
"guinier_point_last": 64,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDG3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
