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{
"code": "SASDEY4",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.",
"publication": {
"title": "Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.",
"author_list": "Bucciarelli S, Midtgaard SR, Nors Pedersen M, Skou S, Arleth L, Vestergaard B",
"journal": "J Appl Crystallogr",
"doi": "10.1107/S1600576718014462",
"pmid": "30546289",
"published_date": "2018 Dec 1"
},
"status": "released",
"submitted_date": "2018-09-29",
"released_date": "2018-11-11"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEY4.d",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEY4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEY4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEY4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "pixel counting",
"name": "Pilatus3 R 300K",
"resolution": 172.0
},
"name": "University of Copenhagen, Department of Drug Design and Pharmacology",
"city": "Copenhagen",
"country": "Denmark",
"beamline_name": "Xenocs BioXolver L with MetalJet",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "Ribonuclease pancreatic",
"short_name": "RNase A",
"sequence": "KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQ\r\nKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHF\r\nDASV",
"organism": "Bos taurus",
"uniprot_code": "P61823",
"uniprot_range_first": 27,
"uniprot_range_last": 150,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRN\nLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPN\nCAYKTTQANKHIIVACEGNPYVPVHFDASV",
"mw": 13.69,
"total_mw": 13.69,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "PBS",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Ribonuclease A monomer from in-house SEC-SAXS",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Copenhagen, Denmark",
"full_name": "University of Copenhagen",
"webpage": "http://www.ku.dk/"
}
],
"contributor_name": "Saskia",
"contributor_surname": "Bucciarelli",
"orcid": "https://orcid.org/0000-0001-7612-223X"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-01-23",
"storage_temperature": null,
"cell_temperature": 23.0,
"exposure_time": 30.0,
"number_of_frames": 11,
"wavelength": 0.134,
"sample_detector_distance": 0.654,
"concentration_min": null,
"concentration_max": 4.2,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.111,
"s_max": 5.022,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY4_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "9rat",
"ext_code": "9RAT",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEY4_fit1_model1.pdb",
"model_mw": 13.69,
"bead_radius": null,
"log": null,
"symmetry": "C1",
"comment": null,
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/9rat_RibA00_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.169,
"p_value": 0.062024,
"fit_residual_plot": "9rat_RibA00_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY4_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/9rat_RibA00.log",
"software_version": null,
"description": "CRYSOL fit of the RNaseA crystal structure (9rat) to the experimental SAXS data"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY4_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "5.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEY4_fit2_model1.pdb",
"model_mw": 5.727,
"bead_radius": 1.25,
"log": "https://www.sasbdb.org/media/log_files/damsel_IQrTwOA.log",
"symmetry": "P1",
"comment": null,
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/RiboA_1_1_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.019,
"p_value": 0.897032,
"fit_residual_plot": "RiboA_1_1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY4_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/RiboA_1_1.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "BayesApp",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "The RNaseA sample (500 microlitres at 7.5 mg/ml) was injected onto a GE Healthcare S200 Increase 10/300 (24 ml) column at a flow rate of 0.1 ml/min at 23°C. A total of 500 x 30 second SAXS data frames were recorded throughout the RNaseA elution. After background solvent corrections, SEC-SAXS data frames 239-249, corresponding to monomeric RNase, were scaled, averaged and binned logarithmically to produce the data displayed in this entry. Additional files, including plots of the selected frames and of I(0), HPLC and exposure cell UV traces and Rg vs. time (determined by AUTORG) are included in the additional files of the full entry zip archive.",
"experiment_description": "SAXS data from solutions of Ribonuclease A monomer from in-house SEC-SAXS in PBS, pH 7.4 were collected on a Xenocs BioXolver L instrument at the Copenhagen University, Department of Drug Design and Pharmacology (Copenhagen, Denmark) using a 20Hz Pilatus 300K detector at a sample-detector distance of 0.7 m and at a wavelength of λ = 0.134 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle).",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 10.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 2.083261,
"pddf_i0_error": 0.00027,
"guinier_i0": 0.166,
"guinier_i0_error": 0.00108,
"pddf_rg": 1.47,
"pddf_rg_error": 0.01,
"guinier_rg": 1.49,
"guinier_rg_error": 0.016,
"pddf_dmax": 4.77,
"pddf_dmax_error": 0.47,
"porod_volume": 10.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 11,
"guinier_point_last": 36,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEY4_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
