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{
"code": "SASDBG7",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions.",
"publication": {
"title": "SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions.",
"author_list": "Santos SP, Cuypers MG, Round A, Finet S, Narayanan T, Mitchell EP, Romão CV",
"journal": "J Mol Biol",
"doi": "10.1016/j.jmb.2017.01.008",
"pmid": "28088481",
"published_date": "2017 Mar 10"
},
"status": "released",
"submitted_date": "2016-11-04",
"released_date": "2017-02-15"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBG7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBG7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBG7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBG7.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": "DNA protection during starvation protein 1",
"short_name": "Dps1",
"sequence": "MTKKSTKSEAASKTKKSGVPETGAQGVRAGGADHADAAHLGTVNNALVNHHYLEEKEFQTVAETLQRNLA\r\nTTISLYLKFKKYHWDIRGRFFRDLHLAYDEFIAEIFPSIDEQAERLVALGGSPLAAPADLARYSTVQVPQ\r\nETVRDARTQVADLVQDLSRVGKGYRDDSQACDEANDPVTADMYNGYAATIDKIRWMLQAIMDDERLD",
"organism": "Deinococcus radiodurans R1",
"uniprot_code": "Q9RS64",
"uniprot_range_first": 1,
"uniprot_range_last": 207,
"oligomerization": "dodecamer",
"molecular_type": "protein",
"uniprot_sequence": "MTKKSTKSEAASKTKKSGVPETGAQGVRAGGADHADAAHLGTVNNALVNHHYLEEKEFQT\nVAETLQRNLATTISLYLKFKKYHWDIRGRFFRDLHLAYDEFIAEIFPSIDEQAERLVALG\nGSPLAAPADLARYSTVQVPQETVRDARTQVADLVQDLSRVGKGYRDDSQACDEANDPVTA\nDMYNGYAATIDKIRWMLQAIMDDERLD",
"mw": 23.02,
"total_mw": 276.24,
"number_molecules": 12,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris-HCl, 150 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Dps1, DNA binding protein under starvation conditions (SEC-SAXS)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Oeiras, Portugal",
"full_name": "Instituto de Tecnologia Química e Biológica António Xavier, Universidade de Lisboa",
"webpage": "http://www.itqb.unl.pt"
}
],
"contributor_name": "Sandra",
"contributor_surname": "Santos",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-11-22",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 1500,
"wavelength": 0.09919,
"sample_detector_distance": 2.80999,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.106,
"s_max": 4.485,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBG7_fit1_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.2i",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBG7_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": null,
"symmetry": "P23",
"comment": "",
"user": 162
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBG7_fit1_fit_img.png",
"software": null,
"chi_square_value": 11.02,
"p_value": 9e-05,
"fit_residual_plot": "SASDBG7_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBG7_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBG7_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBG7_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": null,
"symmetry": "P23",
"comment": "",
"user": 162
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBG7_fit2_fit_img.png",
"software": null,
"chi_square_value": 11.9,
"p_value": 0.0001,
"fit_residual_plot": "fit4columns619_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBG7_fit2.fit",
"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": null,
"experiment_description": "Synchrotron SAXS data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle) were collected from a sample of Dps1, (DNA binding protein under starvation conditions) using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) at the BM29 beam line on the ESRF storage ring (Grenoble, France). Data (1500 successive 1 second frames), were collected using a Pilatus 1M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.09919 nm. The SEC mobile phase consisted of 20 mM Tris-HCl, 150 mM NaCl, pH 7.5, (20°C) with a sample injection concentration of 10 mg/ml. Data obtained from solute-free eluates and SEC-elution peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted from the SEC-peak frames to produce the data displayed in this entry.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 256.97,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 256.97,
"porod_mw_error": null,
"pddf_i0": 50.75,
"pddf_i0_error": 0.04,
"guinier_i0": 50.76,
"guinier_i0_error": 0.12,
"pddf_rg": 4.14,
"pddf_rg_error": 0.004,
"guinier_rg": 4.17,
"guinier_rg_error": 0.16,
"pddf_dmax": 12.75,
"pddf_dmax_error": null,
"porod_volume": 436.85,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 17,
"guinier_point_last": 49,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBG7_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
