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{
"code": "SASDA96",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
"publication": {
"title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
"author_list": "Franke D, Jeffries CM, Svergun DI",
"journal": "Nat Methods",
"doi": "10.1038/nmeth.3358",
"pmid": "25849637",
"published_date": "2015 May"
},
"status": "released",
"submitted_date": null,
"released_date": "2015-05-01"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDA96.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDA96.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA96_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA96_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA96_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA96_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDA96.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": "Lysozyme C",
"short_name": "Lysozyme, lys",
"sequence": "KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA\r\nTNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG\r\nNGMNAWVAWRNRCKGTDVQAWIRGCRL",
"organism": "Gallus gallus",
"uniprot_code": "P00698",
"uniprot_range_first": 19,
"uniprot_range_last": 147,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA\nTNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG\nNGMNAWVAWRNRCKGTDVQAWIRGCRL",
"mw": 14.31,
"total_mw": 14.31,
"number_molecules": 1,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "20 mM Sodium Acetate/HEPES",
"concentration_unit": "mM",
"comment": "Mixed Buffer",
"additive": null,
"concentration": 20.0,
"pka": null,
"ph": 6.8,
"deuteration": null
},
"purity_method": null,
"name": "Lysozyme",
"ext_coefficient": 2.653,
"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": "Daniel",
"contributor_surname": "Franke",
"orcid": null
},
{
"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
},
{
"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": "Dmitri",
"contributor_surname": "Svergun",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2013-02-17",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.12,
"sample_detector_distance": 3.1,
"concentration_min": null,
"concentration_max": 2.61,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.166,
"s_max": 3.789,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDA96_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDA96_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/lyso.log",
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA96_fit1_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.083118,
"p_value": 0.357,
"fit_residual_plot": "SASDA96_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDA96_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDA96_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1lys",
"ext_code": "1lys",
"ext_type": "pdb",
"difference_with_model": null
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDA96_fit2_model1.pdb",
"model_mw": 14.32,
"bead_radius": 0.0,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA96_fit2_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.0792,
"p_value": 0.1536,
"fit_residual_plot": "fit4columns142_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDA96_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDA96_fit3_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1lys",
"ext_code": "1lys",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDA96_fit3_model1.pdb",
"model_mw": 14.32,
"bead_radius": 0.0,
"log": null,
"symmetry": "",
"comment": "",
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA96_fit3_fixed_fit_img.png",
"software": null,
"chi_square_value": 1.047712,
"p_value": 0.0799,
"fit_residual_plot": "fit4columns143_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDA96_fit3.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": "Bovine Serum Albumin",
"description": null,
"experiment_description": "X-ray synchrotron radiation scattering data from a solution of Lysozyme C in 20 mM Sodium Acetate/HEPES, pH 6.8 were collected on the P12 beam line at Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle and λ = 0.12 nm). One solute concentration at 2.61 mg/ml was measured using a total exposure time of 1 second (20 x 0.050 second frames). The data were normalized to the intensity of the transmitted beam and radially averaged. Scattering contributions from the matched solvent blank were subtracted and the resulting 1D scattering data were scaled to protein concentration. The data presented in this entry were obtained from a single concentration scattering curve.",
"tags": [
"benchmark"
],
"intensity_unit": null,
"experimental_mw": 14.8,
"experimental_mw_error": null,
"guinier_i0_mw": 14.8,
"guinier_i0_mw_error": null,
"porod_mw": 13.93,
"porod_mw_error": null,
"pddf_i0": 780.5,
"pddf_i0_error": null,
"guinier_i0": 779.5,
"guinier_i0_error": null,
"pddf_rg": 1.51,
"pddf_rg_error": null,
"guinier_rg": 1.5,
"guinier_rg_error": null,
"pddf_dmax": 4.79,
"pddf_dmax_error": null,
"porod_volume": 23.69,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 260,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": "https://www.sasbdb.org/media/standard_curves/bsa_0006.dat",
"intensities_log_log_plot": "SASDA96_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
