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{
"code": "SASDCT6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.",
"publication": {
"title": "The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.",
"author_list": "Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD",
"journal": "Nucleic Acids Res",
"doi": "10.1093/nar/gky206",
"pmid": "29850894",
"published_date": "2018 Jun 1"
},
"status": "released",
"submitted_date": "2017-08-03",
"released_date": "2018-03-25"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCT6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCT6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCT6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCT6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCT6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCT6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCT6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Pilatus",
"name": "Pilatus 200K",
"resolution": 172.0
},
"name": "Cornell High Energy Synchrotron Source (CHESS)",
"city": "Ithaca, NY",
"country": "USA",
"beamline_name": "G1",
"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": "169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)",
"short_name": "DNA",
"sequence": "CTTTCAGCTGATATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATCTTGATATCAGCTGAAAG",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 52.468,
"total_mw": 52.468,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H2A type 1",
"short_name": "H2A",
"sequence": "MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT\r\nAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK\r\nTESAKSAKSK",
"organism": "Xenopus laevis",
"uniprot_code": "P06897",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT\nAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK\nTESAKSAKSK",
"mw": 13.966,
"total_mw": 13.966,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H2B 1.1",
"short_name": "H2B",
"sequence": "MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM\r\nSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT\r\nKYTSAK",
"organism": "Xenopus laevis",
"uniprot_code": "P02281",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM\nSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT\nKYTSAK",
"mw": 13.934,
"total_mw": 13.934,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H3.2",
"short_name": "H3",
"sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE\r\nLLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI\r\nMPKDIQLARRIRGERA",
"organism": "Xenopus laevis",
"uniprot_code": "P84233",
"uniprot_range_first": 1,
"uniprot_range_last": 136,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE\nLLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI\nMPKDIQLARRIRGERA",
"mw": 15.388,
"total_mw": 15.388,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Histone H4",
"short_name": "H4",
"sequence": "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK\r\nVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
"organism": "Xenopus laevis",
"uniprot_code": "P62799",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK\nVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
"mw": 11.367,
"total_mw": 11.367,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2)",
"concentration_unit": null,
"comment": "60% sucrose ADP-BeF3",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.8,
"deuteration": null
},
"purity_method": null,
"name": "12N12 nucleosome in 60% sucrose with ADP-BeF3",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Ithaca, NY, United States",
"full_name": "Cornell University",
"webpage": "https://www.cornell.edu/"
}
],
"contributor_name": "Joshua",
"contributor_surname": "Tokuda",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-10-24",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 10.0,
"number_of_frames": 40,
"wavelength": 0.1109,
"sample_detector_distance": 2.08,
"concentration_min": null,
"concentration_max": 1.1,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.16,
"s_max": 2.6,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCT6_fit1_model1_img.png",
"software": "Custom in-house",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCT6_fit1_model1.pdb",
"model_mw": 103.9,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": "Generated using 3D-DART and custom scripts written in Pymol. Percentage represents ensemble weight.",
"user": 170
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCT6_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.67,
"p_value": 0.0646,
"fit_residual_plot": "fit4columns1046_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCT6_fit1.fit",
"fit_log": null,
"software_version": "2.1 r7883",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "Version 5.0 (r4547)",
"i0_calibration_standard": null,
"description": "12N12 nucleosome measured in 60% sucrose and ADP-BeF3. \r\nDue to contrast matching between the solvent and histone proteins (due to sucrose), the measured signal is dominated by the DNA component. The model was generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the model key below: \r\nSASDCT6_fit1_model1 = 12N12_ADP_01_100perc",
"experiment_description": "Synchrotron SAXS data from solutions of 12N12 nucleosome in 60% sucrose with ADP-BeF3 in 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2), pH 7.8, were collected on the G1 beam line at the Cornell High Energy Synchrotron Source (Ithaca, NY, USA) using a Pilatus Pilatus 200K detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1109 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 1.10 mg/ml was measured at 25°C. 40 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted to produce the scattering profile displayed in this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 105.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.0222,
"pddf_i0_error": 0.00013,
"guinier_i0": 0.021622,
"guinier_i0_error": 0.000176,
"pddf_rg": 4.937,
"pddf_rg_error": 0.026,
"guinier_rg": 4.812,
"guinier_rg_error": 0.52,
"pddf_dmax": 14.0,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 12,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCT6_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:28:07.375857+02:00",
"bragg_peak": []
}
