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{
"code": "SASDFV5",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.",
"publication": {
"title": "Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.",
"author_list": "Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M",
"journal": "Nat Commun",
"doi": "10.1038/s41467-020-16724-5",
"pmid": "32518228",
"published_date": "2020 Jun 9"
},
"status": "released",
"submitted_date": "2019-04-26",
"released_date": "2020-04-21"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFV5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFV5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFV5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFV5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFV5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFV5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFV5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 X 2M",
"resolution": 172.0
},
"name": "Advanced Light Source (ALS)",
"city": "Berkeley, CA",
"country": "USA",
"beamline_name": "12.3.1 (SIBYLS)",
"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": "80bp_DNA Forward",
"short_name": null,
"sequence": "AATGAGGTAACAACGAAAGCAGATGATAGCTGCTTATCAATTTGTTGCAAACAAGTAGCCGCGCCCAATGAGGTAACAAT",
"organism": "Escherichia coli",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 24.849,
"total_mw": 24.849,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "80bp_DNA Reverse",
"short_name": null,
"sequence": "TTACTCCATTGTTGCTTTCGTCTACTATCGACGAATAGTTAAACAACGTTTGTTCATCGGCGCGGGTTACTCCATTGTTA",
"organism": "Escherichia coli",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 24.612,
"total_mw": 24.612,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "DNA-binding protein HU-alpha",
"short_name": null,
"sequence": "MNKTQLIDVI AEKAELSKTQ AKAALESTLA AITESLKEGD AVQLVGFGTF KVNHRAERTG\r\n RNPQTGKEIK IAAANVPAFV SGKALKDAVK",
"organism": "Escherichia coli",
"uniprot_code": "P0ACF0",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "14-mer",
"molecular_type": "protein",
"uniprot_sequence": "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTG\nRNPQTGKEIKIAAANVPAFVSGKALKDAVK",
"mw": 9.535,
"total_mw": 133.49,
"number_molecules": 14,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM Bis-Tris, 150 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.5,
"deuteration": null
},
"purity_method": null,
"name": "DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 6.5 with 150 mM NaCl",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "UCSF",
"address": "San Francisco, CA, USA",
"full_name": "University of California, San Francisco (UCSF)",
"webpage": "https://www.ucsf.edu/"
}
],
"contributor_name": "Soumya",
"contributor_surname": "G Remesh",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-06-01",
"storage_temperature": null,
"cell_temperature": 10.0,
"exposure_time": 3.0,
"number_of_frames": 300,
"wavelength": 0.103,
"sample_detector_distance": 1.5,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.12,
"s_max": 3.503,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFV5_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/SASDFV5_fit1_model1.pdb",
"model_mw": 152.2,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 293
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFV5_fit1_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 3.177996,
"p_value": 0.0,
"fit_residual_plot": "SASDFV5_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFV5_fit1.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": null,
"experiment_description": "Synchrotron SAXS data from solutions of DNA-binding protein HU-alpha bound to 80 base-pair DNA in 10 mM Bis-Tris, 150 mM NaCl, pH 6.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). 300 successive 3 second frames were collected at 10°C. 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": 300.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 73.39,
"pddf_i0_error": null,
"guinier_i0": 71.81,
"guinier_i0_error": 2.86,
"pddf_rg": 7.64,
"pddf_rg_error": null,
"guinier_rg": 6.956,
"guinier_rg_error": 0.516,
"pddf_dmax": 26.2,
"pddf_dmax_error": null,
"porod_volume": 352.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 13,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFV5_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-06-22T11:01:17.605871+02:00",
"bragg_peak": []
}
