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": "SASDBY4",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.",
"publication": {
"title": "Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.",
"author_list": "Warren C, Matsui T, Karp JM, Onikubo T, Cahill S, Brenowitz M, Cowburn D, Girvin M, Shechter D",
"journal": "Nat Commun",
"doi": "10.1038/s41467-017-02308-3",
"pmid": "29263320",
"published_date": "2017 Dec 20"
},
"status": "released",
"submitted_date": "2016-06-02",
"released_date": "2017-11-18"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBY4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBY4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBY4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBY4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Rayonix MX225-HE",
"resolution": null
},
"name": "Stanford Synchrotron Radiation Lightsource (SSRL)",
"city": "Menlo Park, CA",
"country": "USA",
"beamline_name": "BL4-2",
"beam_geometry": null,
"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": "Nucleoplasmin core + A2",
"short_name": "Npm core",
"sequence": "ASTASNTSKVEKPVSLIWGCELNEQNKTFAFKIEDEEEKCEHQLALRTVCLGDKAKDEFHIVEIVTQEEGKEKPVPIASLKPSILPMATMVGIELTPPVTFRLKAGSGPVYISGQHVAMEEDYSWAEEEDEGEEEEEEEEDPESP",
"organism": "Xenopus laevis",
"uniprot_code": "Q6NUC7",
"uniprot_range_first": 2,
"uniprot_range_last": 145,
"oligomerization": "pentamer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 16.165,
"total_mw": 80.824,
"number_molecules": 5,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H2A (ΔAla127)",
"short_name": "2HA",
"sequence": "SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSKSK",
"organism": "Xenopus laevis",
"uniprot_code": "Q6AZJ8",
"uniprot_range_first": 2,
"uniprot_range_last": 130,
"oligomerization": "pentamer",
"molecular_type": "protein",
"uniprot_sequence": "MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT\nAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK\nTESSKSAKSK",
"mw": 13.879,
"total_mw": 69.395,
"number_molecules": 5,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H2B 1.1 (Ser33Thr)",
"short_name": "H2B",
"sequence": "AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK",
"organism": "Xenopus laevis",
"uniprot_code": "P02281",
"uniprot_range_first": 5,
"uniprot_range_last": 126,
"oligomerization": "pentamer",
"molecular_type": "protein",
"uniprot_sequence": "MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM\nSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT\nKYTSAK",
"mw": 13.494,
"total_mw": 67.468,
"number_molecules": 5,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris. 150 mM NaCl, 1 mM EDTA, 5 mM DTT",
"concentration_unit": "mM",
"comment": null,
"additive": "150mM NaCl, 1mM EDTA, 5mM DTT",
"concentration": 20.0,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Pentameric Nucleoplasmin-histone H2A/H2B complex",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [],
"contributor_name": "Michael",
"contributor_surname": "Brenowitz",
"orcid": null
},
{
"affiliation": [],
"contributor_name": "Sean",
"contributor_surname": "Cahill",
"orcid": null
},
{
"affiliation": [],
"contributor_name": "Mark",
"contributor_surname": "Girvin",
"orcid": null
},
{
"affiliation": [],
"contributor_name": "Jerome",
"contributor_surname": "Karp",
"orcid": null
},
{
"affiliation": [
{
"short_name": "SLAC",
"address": "Menlo Park, CA, USA",
"full_name": "Stanford Synchrotron Radiation Lightsource",
"webpage": "http://www-ssrl.slac.stanford.edu/"
}
],
"contributor_name": "Tsutomu",
"contributor_surname": "Matsui",
"orcid": null
},
{
"affiliation": [],
"contributor_name": "Takashi",
"contributor_surname": "Onikubo",
"orcid": null
},
{
"affiliation": [],
"contributor_name": "David",
"contributor_surname": "Shechter",
"orcid": null
},
{
"affiliation": [],
"contributor_name": "Christopher",
"contributor_surname": "Warren",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-01-07",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 55,
"wavelength": 0.1127,
"sample_detector_distance": 1.7,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.16,
"s_max": 2.994,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY4_fit1_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r6345",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY4_fit1_model1.pdb",
"model_mw": 250.736,
"bead_radius": 5.75,
"log": null,
"symmetry": "P5",
"comment": "",
"user": 131
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBY4_fit2_fit_img.png",
"software": null,
"chi_square_value": 1.58,
"p_value": 0.0,
"fit_residual_plot": "SASDBY4_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY4_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY4_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY4_fit2_model1.pdb",
"model_mw": 223.5,
"bead_radius": 1.9,
"log": null,
"symmetry": "P5",
"comment": null,
"user": 131
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Major_site_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.43,
"p_value": 0.0,
"fit_residual_plot": "Major_site_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY4_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY4_fit3_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY4_fit3_model1.pdb",
"model_mw": 223.5,
"bead_radius": 1.9,
"log": null,
"symmetry": "P5",
"comment": null,
"user": 131
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/Minor_site_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.26,
"p_value": 0.000139,
"fit_residual_plot": "Minor_site_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY4_fit3.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": "The models displayed for this entry are: Top: ab initio bead model representation (derived from individual reconstructions (example fit shown), aligned, spatially averaged and volume-occupancy corrected): Middle: The best CORAL model using the major A2 site (site #1) of A2:H2A/H2B complex as a starting structure (See Figure 5D in the primary citation). Lacking fragments reconstructed by the program CORAL are shown as spheres. Bottom: The best CORAL model using the minor A2 site (site #2) of A2:H2A/H2B complex as a starting structure (See Figure 5D in the primary citation). Lacking fragments reconstructed by the program CORAL are shown as spheres.",
"experiment_description": "Synchrotron SAXS data measured from solutions of the pentameric nucleoplasmin-histone H2A/H2B complex in 20 mM Tris 150mM NaCl, 1mM EDTA, 5mM DTT, pH 8.0, were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (Stanford, USA) using a Rayonix MX225-HE detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.1127 nm). Fifty five successive 1 s data frames were collected immediately after the protein complex eluted from a size-exclusion chromatography (SEC) column. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank (derived from the SEC running solvent) was subtracted and the individual solvent-corrected SAXS profiles were scaled and averaged to produce the final merged SAXS data profile.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 251.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": 251.0,
"pddf_i0": 2822.0,
"pddf_i0_error": 8.0,
"guinier_i0": 2875.52,
"guinier_i0_error": 14.75,
"pddf_rg": 4.32,
"pddf_rg_error": 0.01,
"guinier_rg": 4.39,
"guinier_rg_error": 0.03,
"pddf_dmax": 14.0,
"pddf_dmax_error": null,
"porod_volume": 402.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 16,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBY4_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-08-18T17:28:04.360641+02:00",
"bragg_peak": []
}
