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{
"code": "SASDEF2",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/nm",
"project": {
"title": "Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.",
"publication": {
"title": "Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.",
"author_list": "Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P",
"journal": "Cell",
"doi": "10.1016/j.cell.2018.10.039",
"pmid": "30445040",
"published_date": "2018 Nov 15"
},
"status": "released",
"submitted_date": "2018-08-13",
"released_date": "2018-11-21"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEF2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEF2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEF2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEF2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"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": "Mitochondrial import inner membrane translocase subunit TIM9",
"short_name": "TIM9",
"sequence": "MDALNSKEQQEFQKVVEQKQMKDFMRLYSNLVERCFTDCVNDFTTSKLTNKEQTCIMKCSEKFLKHSERVGQRFQEQNAALGQGLGR",
"organism": "Saccharomyces cerevisiae",
"uniprot_code": "O74700",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "trimer",
"molecular_type": "protein",
"uniprot_sequence": "MDALNSKEQQEFQKVVEQKQMKDFMRLYSNLVERCFTDCVNDFTTSKLTNKEQTCIMKCS\nEKFLKHSERVGQRFQEQNAALGQGLGR",
"mw": 10.202,
"total_mw": 30.606,
"number_molecules": 3,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Mitochondrial import inner membrane translocase subunit TIM10",
"short_name": null,
"sequence": "GSFLGFGGGQPQLSSQQKIQAAEAELDLVTDMFNKLVNNCYKKCINTSYSEGELNKNESSCLDRCVAKYFETNVQVGENMQKMGQSFNAAGKF",
"organism": "Saccharomyces cerevisiae",
"uniprot_code": "P87108",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "trimer",
"molecular_type": "protein",
"uniprot_sequence": "MSFLGFGGGQPQLSSQQKIQAAEAELDLVTDMFNKLVNNCYKKCINTSYSEGELNKNESS\nCLDRCVAKYFETNVQVGENMQKMGQSFNAAGKF",
"mw": 10.23,
"total_mw": 30.69,
"number_molecules": 3,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50mM Tris, 150mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Mitochondrial import inner membrane translocase complex TIM9·10",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL",
"address": "Grenoble, France",
"full_name": "European Molecular Biology Laboratory (EMBL) - Grenoble Outstation",
"webpage": "https://www.embl.fr/"
}
],
"contributor_name": "Martha",
"contributor_surname": "Brennich",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-08-27",
"storage_temperature": 35.0,
"cell_temperature": 20.0,
"exposure_time": 20.0,
"number_of_frames": 1,
"wavelength": 0.099,
"sample_detector_distance": 2.864,
"concentration_min": 1.0,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.06,
"s_max": 4.939,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF2_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "3dxr",
"ext_code": "3DXR",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEF2_fit1_model1.pdb",
"model_mw": 59.45,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/run10_4fajqlt.log",
"symmetry": null,
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEF2_fit1_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.86,
"p_value": 0.0,
"fit_residual_plot": "SASDEF2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF2_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run10_PmRpONj.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF2_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r6669",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEF2_fit2_model1.pdb",
"model_mw": 42.5,
"bead_radius": 2.1,
"log": null,
"symmetry": "C3",
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEF2_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.378,
"p_value": 0.0,
"fit_residual_plot": "SASDEF2_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF2_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dammif10.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF2_fit3_model1_img.png",
"software": "GROMACS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEF2_fit3_model1.pdb",
"model_mw": 61.26,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "The model is a snapshot from the ensemble creating the fit.",
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEF2_fit3_fit_img.png",
"software": "Other",
"chi_square_value": 8.6175,
"p_value": 0.0,
"fit_residual_plot": "SASDEF2_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF2_fit3.FIT",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of the mitochondrial import inner membrane translocase complex (TIM9·10) in 50mM Tris, 150mM NaCl, pH 7.4 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 5 mg/ml were measured at 20°C. One 20 second frame was collected per concentration. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 61.0,
"experimental_mw_error": null,
"guinier_i0_mw": 49.97,
"guinier_i0_mw_error": 10.0,
"porod_mw": 61.0,
"porod_mw_error": null,
"pddf_i0": 50.28,
"pddf_i0_error": null,
"guinier_i0": 49.97,
"guinier_i0_error": 0.03,
"pddf_rg": 2.725,
"pddf_rg_error": null,
"guinier_rg": 2.67,
"guinier_rg_error": 0.01,
"pddf_dmax": 10.0,
"pddf_dmax_error": null,
"porod_volume": 103.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 7,
"guinier_point_last": 91,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEF2_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
