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{
"code": "SASDA59",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Analysis of self-assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus.",
"publication": {
"title": "Analysis of self-assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus.",
"author_list": "Liu J, Falke S, Drobot B, Oberthuer D, Kikhney A, Guenther T, Fahmy K, Svergun D, Betzel C, Raff J",
"journal": "Eur Biophys J",
"doi": "10.1007/s00249-016-1139-9",
"pmid": "27270294",
"published_date": "2017 Jan"
},
"status": "released",
"submitted_date": "2015-07-29",
"released_date": "2016-06-08"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDA59.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDA59.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA59_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA59_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA59_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA59_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDA59.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "S-layer protein",
"short_name": "Slp1",
"sequence": "manqpkkykkfvataatatlvasaivpvasaagfsdvagndhevainalveagiingyad\r\ngtfkpnqsinrgqvvkllgrwleaqgqeipadwetkqrftdlpvtaeaelvkyaalakda\r\ngvfagsngnlnhtqtmqrqqmavvlvraikeissvdlvadykkagfvteitdleaaysae\r\nqrnaivaleyagitnvskfnpassitrgqfasflhrtinnvmepeagvstvkainnttve\r\nvtfdtevdnvqalnflisdlevknaavkqtnkkvvvlttaaqtadkeytvslgedkigtf\r\nkgiaavnptkvemvssatqgklgqqvtvkaqvtvaegqskagipvtfyvpgkndavypti\r\ntgeaftdengvasysytryaagtdavtayatgdrskfatghvfwgvdtilaieevttgat\r\ninnganktykivyknattgkpeanktfnvsflenidvtsnklanatvngvavsqlsnasv\r\nvkaaqittdskgeatftvsgtnaevtpvvfeaeaivtsgsttvtgysqkysasslqttaa\r\nkvkfgalqaeytidvtreggevaargvnngreykvtvkdkdgklakneiinvafnedldr\r\nvistetkayfidvdkddkqtisstpskisvktndkgeatfvigsdkendyatpvawidin\r\nssnakdgqldegepktiaqishfqdayldggavkaylapkfdksvtefkgnetatfkasl\r\nvnqsgkdmpntsiknvtytifntgsndvqvngqvispnrsytvssetlkstdltvtsvng\r\nkttsvkviatgvakntdgkdyaftskeatakftsltdvgtqitadvvevndkelvfagkd\r\npislkdakfyniygaelvgvdafkddlvnnatyatgvvvtftedkdgkkafrvaragteg\r\nkvnvgalkltnaditvasspattttaatasitltvgetlvinnqsytynagagtadanhy\r\nnslvdlagkisadsktggvkavvnagstgldltgnakgenftykigaltavstingvvgk\r\ndavdqqitftfsaavnvkandsvlingtvagtvasvsgskvvvkiaqasaiptttaitaf\r\ntvngtvlkskltnsdvtigsitlk",
"organism": "Lysinibacillus sphaericus",
"uniprot_code": "M4N8T6",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MANQPKKYKKFVATAATATLVASAIVPVASAAGFSDVAGNDHEVAINALVEAGIINGYAD\nGTFKPNQSINRGQVVKLLGRWLEAQGQEIPADWETKQRFTDLPVTAEAELVKYAALAKDA\nGVFAGSNGNLNHTQTMQRQQMAVVLVRAIKEISSVDLVADYKKAGFVTEITDLEAAYSAE\nQRNAIVALEYAGITNVSKFNPASSITRGQFASFLHRTINNVMEPEAGVSTVKAINNTTVE\nVTFDTEVDNVQALNFLISDLEVKNAAVKQTNKKVVVLTTAAQTADKEYTVSLGEDKIGTF\nKGIAAVNPTKVEMVSSATQGKLGQQVTVKAQVTVAEGQSKAGIPVTFYVPGKNDAVYPTI\nTGEAFTDENGVASYSYTRYAAGTDAVTAYATGDRSKFATGHVFWGVDTILAIEEVTTGAT\nINNGANKTYKIVYKNATTGKPEANKTFNVSFLENIDVTSNKLANATVNGVAVSQLSNASV\nVKAAQITTDSKGEATFTVSGTNAEVTPVVFEAEAIVTSGSTTVTGYSQKYSASSLQTTAA\nKVKFGALQAEYTIDVTREGGEVAARGVNNGREYKVTVKDKDGKLAKNEIINVAFNEDLDR\nVISTETKAYFIDVDKDDKQTISSTPSKISVKTNDKGEATFVIGSDKENDYATPVAWIDIN\nSSNAKDGQLDEGEPKTIAQISHFQDAYLDGGAVKAYLAPKFDKSVTEFKGNETATFKASL\nVNQSGKDMPNTSIKNVTYTIFNTGSNDVQVNGQVISPNRSYTVSSETLKSTDLTVTSVNG\nKTTSVKVIATGVAKNTDGKDYAFTSKEATAKFTSLTDVGTQITADVVEVNDKELVFAGKD\nPISLKDAKFYNIYGAELVGVDAFKDDLVNNATYATGVVVTFTEDKDGKKAFRVARAGTEG\nKVNVGALKLTNADITVASSPATTTTAATASITLTVGETLVINNQSYTYNAGAGTADANHY\nNSLVDLAGKISADSKTGGVKAVVNAGSTGLDLTGNAKGENFTYKIGALTAVSTINGVVGK\nDAVDQQITFTFSAAVNVKANDSVLINGTVAGTVASVSGSKVVVKIAQASAIPTTTAITAF\nTVNGTVLKSKLTNSDVTIGSITLK",
"mw": 116.01,
"total_mw": 116.0,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "Water with Ca2+",
"concentration_unit": null,
"comment": null,
"additive": "Ca2+",
"concentration": null,
"pka": null,
"ph": null,
"deuteration": null
},
"purity_method": null,
"name": "slp-B53 with Ca2+",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": false
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Al",
"contributor_surname": "Kikhney",
"orcid": "https://orcid.org/0000-0003-1321-3956"
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2015-06-02",
"storage_temperature": 20.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": 1.0,
"concentration_max": 7.5,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.027,
"s_max": 4.801,
"total_exposure_time": 1.0,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDA59_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r5577",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDA59_fit1_model1.pdb",
"model_mw": 222.0,
"bead_radius": 5.7,
"log": "https://www.sasbdb.org/media/log_files/Ca-d_10.log",
"symmetry": "",
"comment": "",
"user": 4
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA59_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.465,
"p_value": 0.000681,
"fit_residual_plot": "SASDA59_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDA59_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDA59_fit2_model1_img.png",
"software": "SASREF MX",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2.7.1",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDA59_fit2_model1.pdb",
"model_mw": 116.0,
"bead_radius": null,
"log": null,
"symmetry": "P1",
"comment": "~60% by volume",
"user": 4
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDA59_fit2_model2_img.png",
"software": "SASREF MX",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "sasrefmx",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDA59_fit2_model2.pdb",
"model_mw": 232.0,
"bead_radius": null,
"log": null,
"symmetry": "P2",
"comment": "~40% by volume",
"user": 4
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA59_fit2_fit_img.png",
"software": null,
"chi_square_value": 2.37,
"p_value": 0.0,
"fit_residual_plot": "SASDA59_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDA59_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "slp-B53 with Ca",
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 222.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 380.0,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 14239.2,
"guinier_i0_error": null,
"pddf_rg": 6.839,
"pddf_rg_error": null,
"guinier_rg": 6.37,
"guinier_rg_error": 0.72,
"pddf_dmax": 28.12,
"pddf_dmax_error": null,
"porod_volume": 608.57,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 33,
"guinier_point_last": 65,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDA59_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
