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{
"code": "SASDEC8",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Structural Insights into Bacteriophage GIL01 gp7 Inhibition of Host LexA Repressor.",
"publication": {
"title": "Structural Insights into Bacteriophage GIL01 gp7 Inhibition of Host LexA Repressor.",
"author_list": "Caveney NA, Pavlin A, Caballero G, Bahun M, Hodnik V, de Castro L, Fornelos N, Butala M, Strynadka NCJ",
"journal": "Structure",
"doi": "10.1016/j.str.2019.03.019",
"pmid": "31056420",
"published_date": "2019 Jul 2"
},
"status": "released",
"submitted_date": "2018-11-23",
"released_date": "2019-05-06"
},
"pddf_data": null,
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEC8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC8_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEC8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Hybrid Photon Counting (HPC) X-ray detector",
"name": "Rigaku HyPix-3000",
"resolution": 100.0
},
"name": "University of British Columbia",
"city": "Vancouver",
"country": "Canada",
"beamline_name": "Rigaku BioSAXS-2000",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "Bacillus thuringiensis LexA repressor",
"short_name": "LexA",
"sequence": "MLENMEKLTKRQQDILDFIKLKVQEKGYPPSVREIGQAVGLASSSTVHGHLSRLEEKGYI\r\nRRDPTKPRAIEILGEDRMDTETQSVIQVPIVGKVTAGLPITAVESVEEHFPLPASIVSGA\r\nDQVFMLRISGDSMIEAGIFDGDLVVVRQQQSAYNGEIVVALTEDNEATVKRFYKEKDHFR\r\nLQPENSSLEPIILKQVSVIGKVIGVYRDLH",
"organism": "Bacillus thuringiensis",
"uniprot_code": "A0A2B4EEI3",
"uniprot_range_first": 1,
"uniprot_range_last": 210,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MLENMEKLTKRQQDILDFIKLKVQEKGYPPSVREIGQAVGLASSSTVHGHLSRLEEKGYI\nRRDPTKPRAIEILGEDRMDTETQSVIQVPIVGKVTAGLPITAVESVEEHFPLPASIVSGA\nDQVFMLRISGDSMIEAGIFDGDLVVVRQQQSAYNGEIVVALTEDNEATVKRFYKEKDHFR\nLQPENSSLEPIILKQVSVIGKVIGVYRDLH",
"mw": 23.394,
"total_mw": 46.788,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Bacteriophage pGIL01 gp7",
"short_name": "gp7",
"sequence": "MRDKLLDFIIELSQSSKQVVSKSYVIDRLMQVTKEDYKELEKNVEGKKDD",
"organism": "Bacteriophage pGIL01",
"uniprot_code": "Q7WSG2",
"uniprot_range_first": 1,
"uniprot_range_last": 50,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MRDKLLDFIIELSQSSKQVVSKSYVIDRLMQVTKEDYKELEKNVEGKKDD",
"mw": 5.921,
"total_mw": 23.684,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Hepes, 300 mM NaCl, 10% glycerol,",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Bacillus thuringiensis LexA repressor bound to Bacteriophage pGIL01 gp7 (Bt_LexA_GIL01_gp7)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Vancouver, Canada",
"full_name": "University of British Columbia",
"webpage": "https://www.ubc.ca/"
}
],
"contributor_name": "Nathanael",
"contributor_surname": "Caveney",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-08-25",
"storage_temperature": 6.0,
"cell_temperature": 6.0,
"exposure_time": 300.0,
"number_of_frames": 12,
"wavelength": 0.154,
"sample_detector_distance": null,
"concentration_min": 0.75,
"concentration_max": 12.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.117,
"s_max": 6.422,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC8_fit1_model1_img.png",
"software": "Chimera",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEC8_fit1_model1.pdb",
"model_mw": 59.42,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex",
"user": 389
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/LexA_gp7_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 6.158,
"p_value": 0.0,
"fit_residual_plot": "LexA_gp7_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC8_fit1.fit",
"fit_log": null,
"software_version": null,
"description": "I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC8_fit2_model1_img.png",
"software": "Chimera",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEC8_fit2_model1.pdb",
"model_mw": 59.42,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex in SREFLEX, restrained",
"user": 389
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/rc01_LgiSRAn_fit_img.png",
"software": "SREFLEX",
"chi_square_value": 2.58,
"p_value": 2e-06,
"fit_residual_plot": "rc01_LgiSRAn_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC8_fit2.fit",
"fit_log": null,
"software_version": null,
"description": "I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex in SREFLEX, restrained"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC8_fit3_model1_img.png",
"software": "Chimera",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEC8_fit3_model1.pdb",
"model_mw": 59.42,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex in SREFLEX, unrestrained",
"user": 389
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/uc01_m3mT2gz_fit_img.png",
"software": "SREFLEX",
"chi_square_value": 1.899,
"p_value": 4e-05,
"fit_residual_plot": "uc01_m3mT2gz_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC8_fit3.fit",
"fit_log": null,
"software_version": null,
"description": "I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex in SREFLEX, unrestrained"
}
],
"estimated_volume_method": null,
"pddf_software": null,
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "SAXS data from solutions of Bacillus thuringiensis LexA repressor bound to Bacteriophage pGIL01 gp7 (Bt_LexA_GIL01_gp7) in 20 mM HEPES, 300 mM NaCl, 10% glycerol, pH 8 were collected on a Rigaku BioSAXS-2000 instrument at the University of British Columbia (Vancouver, Canada) using a Hybrid Pixel Array Detector Rigaku HyOix-3000 detector at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 12 mg/ml were measured at 6°C. 12 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 108.2,
"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": 1.53,
"guinier_i0_error": null,
"pddf_rg": null,
"pddf_rg_error": null,
"guinier_rg": 4.391,
"guinier_rg_error": null,
"pddf_dmax": null,
"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": "SASDEC8_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
