{
"code": "SASDEX9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": " EFAMIX\n , a tool to decompose inline chromatography SAXS\n data from partially overlapping components",
"publication": {
"title": " EFAMIX\n , a tool to decompose inline chromatography SAXS\n data from partially overlapping components",
"author_list": "Konarev P, Graewert M, Jeffries C, Fukuda M, Cheremnykh T, Volkov V, Svergun D",
"journal": "Protein Science",
"doi": "10.1002/pro.4237",
"pmid": null,
"published_date": "2021 Nov 22"
},
"status": "released",
"submitted_date": "2021-01-17",
"released_date": "2021-11-24"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEX9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEX9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEX9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEX9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"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": "HpcH/HpaI aldolase",
"short_name": null,
"sequence": "MHHHHHHNKVRTCWNEGRPALAGWLQLPGTLHAEALARLDYDAVVIDMQHSPIDFGQVAPMLIAIELGGAEPFVRTQV\r\nNDPSDIMKLLDAGAYGIIAPMVNTRAEAQTLASALHYSPRGLRSFGPRRPSLRYGSGYLAQASETVVGLAMIETREAL\r\nANIDEILSVDGIDGVFIGPTDLALDLGHAPLVDTEEAEVVSAIAHVRERAHAAGKRVGIFCGSGGFARVKLAEGFDFV\r\nTAAPDLAMLSAAARQVIADARAL",
"organism": "Rhizorhabdus wittichii RW1",
"uniprot_code": "A5VH82",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "hexamer",
"molecular_type": "protein",
"uniprot_sequence": "MNKVRTCWNEGRPALAGWLQLPGTLHAEALARLDYDAVVIDMQHSPIDFGQVAPMLIAIE\r\nLGGAEPFVRTQVNDPSDIMKLLDAGAYGIIAPMVNTRAEAQTLASALHYSPRGLRSFGPR\r\nRPSLRYGSGYLAQASETVVGLAMIETREALANIDEILSVDGIDGVFIGPTDLALDLGHAP\r\nLVDTEEAEVVSAIAHVRERAHAAGKRVGIFCGSGGFARVKLAEGFDFVTAAPDLAMLSAA\r\nARQVIADARAL",
"mw": 27.435,
"total_mw": 164.61,
"number_molecules": 6,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Construct contains a N-terminal polyhistidine tag (MHHHHHH)."
}
],
"buffer": {
"name": "20 mM HEPES,",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Class II pyruvate aldolase (HpcH/HpaI aldolase), wild-type hexamer in HEPES isolated using SEC-SAXS",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"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": "Cy M",
"contributor_surname": "Jeffries",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-11-23",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 51,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 8.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.091,
"s_max": 7.253,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEX9_fit1_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEX9_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": null,
"symmetry": "P32",
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX9_fit1_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.07,
"p_value": 0.158445,
"fit_residual_plot": "SASDEX9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEX9_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/9.log",
"software_version": "2.31",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEX9_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6r62",
"ext_code": "6R62",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "PDB",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEX9_fit2_model1.pdb",
"model_mw": 160.5,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/6R62_hexamerr_noMg00.log",
"symmetry": null,
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX9_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.094,
"p_value": 0.0121,
"fit_residual_plot": "SASDEX9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEX9_fit2.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The quoted experimental MW is that determined from MALLS.",
"experiment_description": "Synchrotron SAXS data from solutions of hydroxypyruvate aldolase in 20 mM HEPES, pH 7.5 were collected using size exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (Hamburg, Germany) equipped with a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The SEC parameters were as follows: An 80 μl sample at 8 mg/ml was injected at room temperature onto a GE Healthcare Superdex 200 Increase 10/300 column at a flow rate of 0.4 mL/min. 51 successive 1 second frames were collected through the lagging region of the SEC-elution peak that corresponded to the molecular weight (MW) of the hexamer (as assessed using multi-angle laser light scattering/refractive index measurements; MALLS/RI). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted and the data scaled and averaged to produce the final SAXS profile displayed in this entry. CHROMIXS was used to process the SEC-SAXS data and assess the MW and Rg through the SEC peak (Rg and MW estimates and unsubtracted individual SEC-SAXS data frames are included in the full entry zip archive).",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 157.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 146.0,
"porod_mw_error": null,
"pddf_i0": 1324.0,
"pddf_i0_error": null,
"guinier_i0": 1320.69,
"guinier_i0_error": 2.0,
"pddf_rg": 3.325,
"pddf_rg_error": null,
"guinier_rg": 3.34,
"guinier_rg_error": 0.01,
"pddf_dmax": 9.35,
"pddf_dmax_error": null,
"porod_volume": 233.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 19,
"guinier_point_last": 110,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEX9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:55:24.740692+02:00",
"bragg_peak": []
}