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": "SASDFX3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.",
"publication": {
"title": "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.",
"author_list": "Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A",
"journal": "Cell Rep",
"doi": "10.1016/j.celrep.2019.03.061",
"pmid": "30970244",
"published_date": "2019 Apr 9"
},
"status": "released",
"submitted_date": "2019-03-12",
"released_date": "2019-04-16"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFX3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFX3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFX3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFX3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFX3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFX3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFX3.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": "Histone H3",
"short_name": "H3",
"sequence": "ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR\r\nLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA",
"organism": "Xenopus laevis",
"uniprot_code": null,
"uniprot_range_first": 2,
"uniprot_range_last": 136,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 15.271,
"total_mw": 30.542,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H4",
"short_name": "H4",
"sequence": "SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDA\r\nVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
"organism": "Xenopus laevis",
"uniprot_code": "P62799",
"uniprot_range_first": 2,
"uniprot_range_last": 103,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK\nVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
"mw": 11.236,
"total_mw": 22.472,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H2a",
"short_name": "H2a",
"sequence": "SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA\r\nARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK",
"organism": "Xenopus laevis",
"uniprot_code": "Q6AZJ8",
"uniprot_range_first": 2,
"uniprot_range_last": 130,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT\nAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK\nTESSKSAKSK",
"mw": 13.95,
"total_mw": 27.9,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H2b",
"short_name": "H2b",
"sequence": "AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFER\r\nIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK",
"organism": "Xenopus laevis",
"uniprot_code": "Q92130",
"uniprot_range_first": 5,
"uniprot_range_last": 126,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM\nSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT\nKYTSAK",
"mw": 13.494,
"total_mw": 26.988,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "147bp 601 Widom sequence",
"short_name": "601-147bp",
"sequence": "ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 45.202,
"total_mw": 45.202,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "15 mM HEPES, 200 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.3,
"deuteration": null
},
"purity_method": null,
"name": "Semi-synthetic nucleosome core particle (NCP)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Italy",
"full_name": "University of Pavia",
"webpage": "http://wcm-3.unipv.it"
}
],
"contributor_name": "Federico",
"contributor_surname": "Forneris",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-12-11",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 243,
"wavelength": 0.1,
"sample_detector_distance": 2.87,
"concentration_min": null,
"concentration_max": 1.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.071,
"s_max": 2.852,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [],
"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 a semi-synthetic nucleosome core particle (NCP) in 15 mM HEPES, 200 mM NaCl, pH 7.3 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column: Wyatt WTC-030N5; Flow rate: 0.25 mL/min; Sample injection concentration: 2.5 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the sample as a series of 243 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 200.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 90.55,
"pddf_i0_error": null,
"guinier_i0": 91.26,
"guinier_i0_error": 0.1,
"pddf_rg": 4.268,
"pddf_rg_error": null,
"guinier_rg": 4.35,
"guinier_rg_error": 0.01,
"pddf_dmax": 12.8,
"pddf_dmax_error": null,
"porod_volume": 353.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 15,
"guinier_point_last": 56,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFX3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
