{ "code": "SASDC39", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Rev7 dimerization is important for assembly and function of the Rev1/PolĪ¶ translesion synthesis complex.", "publication": { "title": "Rev7 dimerization is important for assembly and function of the Rev1/PolĪ¶ translesion synthesis complex.", "author_list": "Rizzo AA, Vassel FM, Chatterjee N, D'Souza S, Li Y, Hao B, Hemann MT, Walker GC, Korzhnev DM", "journal": "Proc Natl Acad Sci U S A", "doi": "10.1073/pnas.1801149115", "pmid": "30111544", "published_date": "2018 Aug 28" }, "status": "released", "submitted_date": "2017-11-14", "released_date": "2018-07-31" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC39.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC39.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC39_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC39_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC39_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC39_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC39.sascif", "experiment": { "instrument": { "detector": { "type": "CCD", "name": "Finger Lakes CCD", "resolution": 0.0 }, "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": "Mitotic spindle assembly checkpoint protein MAD2B", "short_name": "hRev7-WT dimer", "sequence": "GMTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPEL\r\nNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVE\r\nQLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVH\r\nMHDPRLIPLKTMTSDILKMQLYVEERAHKGS", "organism": "Homo sapiens", "uniprot_code": "Q9UI95", "uniprot_range_first": 1, "uniprot_range_last": 211, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPEL\nNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVE\nQLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVH\nMHDPRLIPLKTMTSDILKMQLYVEERAHKGS", "mw": 24.391, "total_mw": 48.782, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "DNA polymerase zeta catalytic subunit", "short_name": "Rev3-RBM2", "sequence": "MEDK KIVIMPCKCA PSRQLVQVWL QAKE", "organism": "Homo sapiens", "uniprot_code": "O60673", "uniprot_range_first": 1988, "uniprot_range_last": 2014, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": 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"mw": 3.273, "total_mw": 3.273, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES, 10 mM DTT, 5% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Human Rev7 dimer in complex with Rev3 peptide @ 9.1mg/mL", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Storrs, CT, USA", "full_name": "University of Connecticut", "webpage": "https://uconn.edu/" } ], "contributor_name": "Alex", "contributor_surname": "Rizzo", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-05-14", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.1267, "sample_detector_distance": null, "concentration_min": null, "concentration_max": 9.1, "sample_volume": null, "flow_rate": null, "s_min": 0.086, "s_max": 8.019, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC39_fit1_model1_img.png", "software": "HADDOCK", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC39_fit1_model1.pdb", "model_mw": 55.07, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "residues at N- and C-termini that were missing in PDB were built in extended conformation", "user": 249 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC39_fit1_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 28.85768, "p_value": 0.0, "fit_residual_plot": "SASDC39_fit1_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC39_fit1.dat", "fit_log": null, "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "Model was created by mapping the dimer interface by mutagenesis (9 residues identified) and then docking the dimer with HADDOCK and the mutations. SAXS/WAXS was used for cross-validation.", "experiment_description": null, "tags": [], "intensity_unit": null, "experimental_mw": 53.7, "experimental_mw_error": null, "guinier_i0_mw": 53.7, "guinier_i0_mw_error": 0.04, "porod_mw": 63.2, "porod_mw_error": null, "pddf_i0": 0.326, "pddf_i0_error": 0.0003, "guinier_i0": 0.324, "guinier_i0_error": 0.00022, "pddf_rg": 3.06, "pddf_rg_error": 0.005, "guinier_rg": 2.98, "guinier_rg_error": 0.003, "pddf_dmax": 11.4, "pddf_dmax_error": null, "porod_volume": 107.4, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 61, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDC39_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }