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.
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{
"code": "SASDGB3",
"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/SASDGB3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB3_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGB3.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, E34K",
"short_name": null,
"sequence": "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITKSLKEGDAVQLVGFGTFKVNHRAERTG\r\nRNPQTGKEIKIAAANVPAFVSGKALKDAVK",
"organism": "Escherichia coli",
"uniprot_code": "P0ACF0",
"uniprot_range_first": 1,
"uniprot_range_last": 90,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTG\nRNPQTGKEIKIAAANVPAFVSGKALKDAVK",
"mw": 9.534,
"total_mw": 19.068,
"number_molecules": 2,
"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, E34K mutant bound to 80 bp DNA (pH 4.5)",
"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": "2018-11-02",
"storage_temperature": 10.0,
"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": 0.081,
"s_max": 3.91,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [],
"estimated_volume_method": null,
"pddf_software": null,
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "This curve is part of a pH series. Increasing the pH removes aggregation presumably due to protein surface charge changes. The SAXS data for this entry is measured from aggregated material and therefore the Rg and I(0) parameters do not apply.",
"experiment_description": "Synchrotron SAXS data from solutions of DNA-binding protein HU-alpha (E34K mutant) bound to 80 bp 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; 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": 65.0,
"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": "SASDGB3_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-06-22T11:00:41.307909+02:00",
"bragg_peak": []
}
