The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDF36",
"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": null,
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF36.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF36_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF36_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF36_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF36.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": "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK",
"organism": "Escherichia coli",
"uniprot_code": "P0ACF0",
"uniprot_range_first": 1,
"uniprot_range_last": 90,
"oligomerization": "unknown",
"molecular_type": "protein",
"uniprot_sequence": "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTG\nRNPQTGKEIKIAAANVPAFVSGKALKDAVK",
"mw": 9.535,
"total_mw": 9.535,
"number_molecules": 0,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM sodium acetate, 50 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 4.5,
"deuteration": null
},
"purity_method": null,
"name": "DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 4.5 with 50 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": "2018-05-27",
"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": 0.092,
"s_max": 3.503,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [],
"estimated_volume_method": null,
"pddf_software": null,
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "SAXS profile corresponds to a protein-DNA complex between bacterial nucleoid associated protein HUalpha and 80bp DNA. Under these conditions, the complex forms lamellar structures visible as Bragg Diffraction peaks.",
"experiment_description": "Synchrotron SAXS data from solutions of DNA-binding protein HU-alpha bound to 80 base-pair DNA in 10 mM sodium acetate, 50 mM NaCl, pH 4.5 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": 350.0,
"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": null,
"guinier_i0_error": null,
"pddf_rg": 2.0,
"pddf_rg_error": null,
"guinier_rg": null,
"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": "SASDF36_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-06-22T11:01:37.606693+02:00",
"bragg_peak": []
}
