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{
"code": "SASDDX9",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "mPAC Delta132",
"publication": null,
"status": "released",
"submitted_date": "2018-07-25",
"released_date": "2021-09-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDX9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDX9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDX9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDX9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDX9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDX9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDX9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Swiss Light Source",
"city": "Villigen",
"country": "Switzerland",
"beamline_name": "cSAXS",
"beam_geometry": null,
"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": "PAS fold family",
"short_name": "mPAC",
"sequence": "GAMGSQAYRKGVQETVKLRDQAIAASSVGIVIADARLPDMPLIYVNPAFEEITGYSDAEVLGYNCRFLQGKDTSQPAVDQLRAAIKAGENCTVTLLNYRKDGTPFWNELTISPIYDDHNNLTHFVGIQSDISDRIKAEQALRLEQEKSERLLLNILPKPIVDQLKQFEGSLAQQFTEATILFADIVGFTQLSAQMSPLELLNLLNNIFSVFDKLAEKHGIEKIKTIGDAYMAVAGLPVANDHHAEAIANMALDMQQAIQQFKTPQGEPFQIRIGINTGLVVAGVIGIKKFSYDLWGDAVNVASRMESSGLPGKIQVTAATKERLQDKYVFEKRGAIVVKGKGEMINYWLVGKQE",
"organism": "Coleofasciculus chthonoplastes PCC 7420",
"uniprot_code": "B4VKN6",
"uniprot_range_first": 133,
"uniprot_range_last": 483,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MNPSCEENEPNLFHGEASLQAFFDLSAELLCIRDSNGYFREINSVWEKTLGWTLDELRSR\nPWLEFVHPDDVAFTFDMENQCHTLQDNKTPICLKNRFRCRDGSYRWLSWRLGAYQNSVSH\nGIAHDVTESNWRGSQAYRKGVQETVKLRDQAIAASSVGIVIADARLPDMPLIYVNPAFEE\nITGYSDAEVLGYNCRFLQGKDTSQPAVDQLRAAIKAGENCTVTLLNYRKDGTPFWNELTI\nSPIYDDHNNLTHFVGIQSDISDRIKAEQALRLEQEKSERLLLNILPKPIVDQLKQFEGSL\nAQQFTEATILFADIVGFTQLSAQMSPLELLNLLNNIFSVFDKLAEKHGIEKIKTIGDAYM\nAVAGLPVANDHHAEAIANMALDMQQAIQQFKTPQGEPFQIRIGINTGLVVAGVIGIKKFS\nYDLWGDAVNVASRMESSGLPGKIQVTAATKERLQDKYVFEKRGAIVVKGKGEMINYWLVG\nKQE",
"mw": 39.015,
"total_mw": 78.03,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 5 % w/v Glycerol, 1 mM ApCpp",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "PAS fold family protein mPAC-Δ132 with the addition of adenosine-5'-[(α,β)-methyleno]triphosphate in the dark state (mPAC-Δ132, dark + ApCpp)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Germany",
"full_name": "Max Planck Institute for Medical Research",
"webpage": "http://www.mpimf-heidelberg.mpg.de/en"
}
],
"contributor_name": "Robert",
"contributor_surname": "Lindner",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-03-11",
"storage_temperature": 0.0,
"cell_temperature": 10.0,
"exposure_time": 0.5,
"number_of_frames": 200,
"wavelength": 0.11,
"sample_detector_distance": 2.13,
"concentration_min": 5.1,
"concentration_max": 9.1,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.16,
"s_max": 2.744,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDX9_fit1_model1_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDX9_fit1_model1.pdb",
"model_mw": 75.06,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 330
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDX9_fit1_fitfoxs_img.png",
"software": "FoXS",
"chi_square_value": 16.481153,
"p_value": 0.0,
"fit_residual_plot": "SASDDX9_fit1_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDX9_fit1.dat",
"fit_log": null,
"software_version": "2",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDX9_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.8.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDX9_fit2_model1.pdb",
"model_mw": 59.655,
"bead_radius": 3.25,
"log": null,
"symmetry": null,
"comment": null,
"user": 330
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDX9_fit2_model2_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.8.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDX9_fit2_model2.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 330
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDX9_fit2_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 52.36,
"p_value": 0.0,
"fit_residual_plot": "SASDDX9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDX9_fit2.fir",
"fit_log": null,
"software_version": "2.8.1",
"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 measurements (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle; λ = 0.11 nm) were carried out at the beam line X12SA of the Swiss Light Source (Paul Scherrer Institut, Villigen, Switzerland). Quartz capillaries (inner diameter 1 mm) were mounted in a sample holder and filled with buffer (20 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 5 % w/v glycerol, 1 mM ApCpp, pH 7.5). The sample holder was cooled to 10 °C for all measurements. Scattering of the buffer was determined at 20 positions along the capillary (spacing 0.5 mm), exposing each position with 11.2 keV photons for 0.5 s using 200 successive frames. Each position was measured 10 times and scattering intensities, after radial averaging to produce 1D-scattering patterns, were averaged. Scattered X-rays were detected by a Pilatus 2M detector (Dectris, Baden-Dättwil, Switzerland) at the end of an evacuated flight tube, 2.13 m from the sample position. Buffer was replaced by the protein sample without moving the sample holder or the capillaries. Lights in the experimental hutch were switched off and after 5 minutes, scattering of the protein-containing solutions was measured at the same positions using the procedure described above. Solute concentrations ranging between 5.1 and 9.1 mg/ml were measured and the concentration series data extrapolated to infinite dilution generating the final SAXS profile displayed in this entry. GASBOR was run 10 times to generate bead-model reconstructions (an averaged representation, top, and individual model, bottom).",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 83.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 7.849,
"pddf_i0_error": null,
"guinier_i0": 8.29,
"guinier_i0_error": 0.017,
"pddf_rg": 3.81,
"pddf_rg_error": null,
"guinier_rg": 3.95,
"guinier_rg_error": 0.19,
"pddf_dmax": 12.8,
"pddf_dmax_error": null,
"porod_volume": 99.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 12,
"guinier_point_last": 35,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDX9_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-09-20T13:38:19.096872+02:00",
"bragg_peak": []
}
