{ "code": "SASDD35", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Elliptical structure of phospholipid bilayer nanodiscs encapsulated by scaffold proteins: casting the roles of the lipids and the protein.", "publication": { "title": "Elliptical structure of phospholipid bilayer nanodiscs encapsulated by scaffold proteins: casting the roles of the lipids and the protein.", "author_list": "Skar-Gislinge N, Simonsen JB, Mortensen K, Feidenhans'l R, Sligar SG, Lindberg Møller B, Bjørnholm T, Arleth L", "journal": "J Am Chem Soc", "doi": "10.1021/ja1030613", "pmid": "20828154", "published_date": "2010 Oct 6" }, "status": "released", "submitted_date": "2018-03-14", "released_date": "2018-04-10" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD35.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD35.rad", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD35_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD35_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD35_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD35_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD35.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "ID14-3", "beam_geometry": "", "type_of_source": "X-ray synchrotron", "point_source": true, "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": "Membrane scaffold protein 1D1", "short_name": "MSP1D1", "sequence": "MGHHHHHHHDYDIPTTENLYFQGSTFSKLREQLGPVTQEFWDNLEKETEGLRQEM\r\nSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQE\r\nKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEY\r\nHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ", "organism": "unidentified", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 24.793, "total_mw": 49.586, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris, 100 mM NaCl, 100 mM sodium cholate,", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Nanodiscs with membrane scaffold protein 1D1 (MSP1D1) and dilaurylphosphatidyl choline (DLPC)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Copenhagen, Denmark", "full_name": "University of Copenhagen", "webpage": "http://www.ku.dk/" } ], "contributor_name": "Andreas", "contributor_surname": "Larsen", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2009-11-14", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.093, "sample_detector_distance": 1.83, "concentration_min": 0.0, "concentration_max": null, "sample_volume": null, "flow_rate": null, "s_min": 0.094, "s_max": 3.82, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD35_fit1_fixed_fit_img.png", "software": "WillItFit", "chi_square_value": 6.5481, "p_value": 0.178409, "fit_residual_plot": "SASDD35_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD35_fit1.fit", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "The entry shows the scattering results obtained from nanodiscs with membrane scaffold protein 1D1 (MSP1D1), a derivative of Apolipoprotein A-I from an unknown organism, and 1,2-dilauroyl-sn-glycero-3-phoshocholine (DLPC). The molecular weight cannot be obtained for these composite protein-lipid particles prior to modelling and therefore the experimental molecular weight remains unknown and is not record for this entry. The expected molecular weight quoted above refers to the dimeric form of the protein component of the nanodiscs, without taking into account the bound DLPC. The probable distribution of real-space distances (or PDDF) and associated structural parameters calculated using BayesApp are included the full entry-zip archive. The fit of the model (not shown) was assessed using WillItFit.", "experiment_description": "Synchrotron SAXS data from solutions of nanodiscs with membrane scaffold protein 1D1 (MSP1D1) and dilaurylphosphatidyl choline (DLPC) in 20 mM Tris, 100 mM NaCl, 100 mM sodium cholate, pH 7.4, were collected on the ID14-3 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.093 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Data were collected at 20°C. 10 successive 1 second frames were recorded. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.", "tags": [], "intensity_unit": "1/cm", "experimental_mw": 0.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.0628, "pddf_i0_error": 0.0001, "guinier_i0": 0.065, "guinier_i0_error": 0.0005, "pddf_rg": 4.6, "pddf_rg_error": 0.02, "guinier_rg": 4.9, "guinier_rg_error": 0.3, "pddf_dmax": 12.15, "pddf_dmax_error": 0.8, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 38, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDD35_datloglog_img.png", "symmetry": null, "last_modified": "2021-01-28T12:14:59.069195+01:00", "bragg_peak": [] }