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{
"code": "SASDDH3",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius.",
"publication": {
"title": "Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius.",
"author_list": "Vogt MS, Völpel SL, Albers SV, Essen LO, Banerjee A",
"journal": "Acta Crystallogr D Struct Biol",
"doi": "10.1107/S2059798318014146",
"pmid": "30387769",
"published_date": "2018 Nov 1"
},
"status": "released",
"submitted_date": "2018-02-08",
"released_date": "2018-12-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDH3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDH3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDH3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDH3.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": "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)",
"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": "2016-05-05",
"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": 0.83,
"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/SASDDH3_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/SASDDH3_fit1_model1.pdb",
"model_mw": 40.8,
"bead_radius": 2.1,
"log": "https://www.sasbdb.org/media/log_files/Dammin_1st_Saci1223_apo-12.log",
"symmetry": null,
"comment": null,
"user": 255
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDH3_fit1_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.376,
"p_value": 0.101902,
"fit_residual_plot": "SASDDH3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH3_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Dammin_1st_Saci1223_apo-12.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDH3_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6cmv",
"ext_code": "6CMV",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDH3_fit2_model1.pdb",
"model_mw": 25.95,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/Saci1223_Dimer00_tKyX31C.log",
"symmetry": null,
"comment": null,
"user": 255
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Saci1223_Dimer0004_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.052,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH3_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Saci1223_Dimer00_zHQDNPu.log",
"software_version": null,
"description": ""
},
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Saci1223_Dimer0004-1_fit_img.png",
"software": "SASREF",
"chi_square_value": 1.05,
"p_value": 0.0,
"fit_residual_plot": "Saci1223_Dimer0004-1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH3_fit3.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The associated atomic model structure is included for comparative purposes only, i.e., to compare the overall topology of the atomic model with the solution scattering and the DAMMIF bead model. Two fits displayed for the atomic model were calculated using CRYSOL (top) and SASREF (bottom).",
"experiment_description": "Synchrotron SAXS data from solutions of Archaeal biofilm regulator 2 (AbfR2) 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 0.83 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": 39.0,
"experimental_mw_error": null,
"guinier_i0_mw": 39.29,
"guinier_i0_mw_error": null,
"porod_mw": 37.0,
"porod_mw_error": null,
"pddf_i0": 24.03,
"pddf_i0_error": null,
"guinier_i0": 24.16,
"guinier_i0_error": 0.09,
"pddf_rg": 2.8,
"pddf_rg_error": null,
"guinier_rg": 2.85,
"guinier_rg_error": 0.03,
"pddf_dmax": 10.0,
"pddf_dmax_error": null,
"porod_volume": 56.89,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 16,
"guinier_point_last": 72,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDH3_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-08-18T17:26:54.233719+02:00",
"bragg_peak": []
}
