{ "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": [] }