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{
"code": "SASDEC9",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in <i>Escherichia coli</i>.",
"publication": {
"title": "Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in <i>Escherichia coli</i>.",
"author_list": "Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.RA119.009739",
"pmid": "31836667",
"published_date": "2020 Jan 17"
},
"status": "released",
"submitted_date": "2018-12-19",
"released_date": "2019-12-13"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEC9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEC9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEC9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEC9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Shanghai Synchrotron Radiation Facility (SSRF)",
"city": "Shanghai",
"country": "China",
"beamline_name": "BL19U2",
"beam_geometry": "",
"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": "Flagellar brake protein YcgR in complex with c-di-GMP",
"short_name": "YcgR-c-di-GMP",
"sequence": "MSHYHEQFLKQNPLAVLGVLRDLHKAAIPLRLSWNGGQLISKLLAITPDKLVLDFGSQAEDNIAVLKAQH\r\nITITAETQGAKVEFTVEQLQQSEYLQLPAFITVPPPTLWFVQRRRYFRISAPLHPPYFCQTKLADNSTLR\r\nFRLYDLSLGGMGALLETAKPAELQEGMRFAQIEVNMGQWGVFHFDAQLISISERKVIDGKNETITTPRLS\r\nFRFLNVSPTVERQLQRIIFSLEREAREKADKVRDKLAAALEHHHHHH",
"organism": "Escherichia coli",
"uniprot_code": "P76010",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSHYHEQFLKQNPLAVLGVLRDLHKAAIPLRLSWNGGQLISKLLAITPDKLVLDFGSQAE\nDNIAVLKAQHITITAETQGAKVEFTVEQLQQSEYLQLPAFITVPPPTLWFVQRRRYFRIS\nAPLHPPYFCQTKLADNSTLRFRLYDLSLGGMGALLETAKPAELQEGMRFAQIEVNMGQWG\nVFHFDAQLISISERKVIDGKNETITTPRLSFRFLNVSPTVERQLQRIIFSLEREAREKAD\nKVRD",
"mw": 29.376,
"total_mw": 29.376,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES, 150mM NaCl, 10% glycerol,",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Flagellar brake protein YcgR in complex with c-di-GMP from Escherichia coli",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "China",
"full_name": "Institute of Biophysics, Chinese Academy of Sciences",
"webpage": "http://english.ibp.cas.cn/"
}
],
"contributor_name": "Yanjie",
"contributor_surname": "Hou",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-01-04",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 1.0,
"number_of_frames": 20,
"wavelength": 0.103,
"sample_detector_distance": null,
"concentration_min": 0.6,
"concentration_max": 4.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.128,
"s_max": 4.546,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC9_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEC9_fit1_model1.pdb",
"model_mw": 26.5,
"bead_radius": 2.6,
"log": null,
"symmetry": null,
"comment": null,
"user": 399
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEC9_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.841,
"p_value": 0.00032,
"fit_residual_plot": "SASDEC9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC9_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Merge22and28-14.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC9_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "5y6f",
"ext_code": "5Y6F",
"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/SASDEC9_fit2_model1.pdb",
"model_mw": 28.16,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/YcgR_refine_64cut03_crysol_DeN0hXa.log",
"symmetry": null,
"comment": null,
"user": 399
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEC9_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.231,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/YcgR_refine_64cut03_crysol.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of the flagellar brake protein, YcgR, in bound to cyclic-di-GMP in 20 mM HEPES, 150mM NaCl, 10% glycerol, pH 7.5 were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Pilatus 1M detector at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.6 and 4.8 mg/ml were measured at 4°C. 20 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 28.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 27.6,
"porod_mw_error": null,
"pddf_i0": 2780.0,
"pddf_i0_error": null,
"guinier_i0": 2755.43,
"guinier_i0_error": 10.9,
"pddf_rg": 2.25,
"pddf_rg_error": null,
"guinier_rg": 2.19,
"guinier_rg_error": 0.06,
"pddf_dmax": 7.25,
"pddf_dmax_error": null,
"porod_volume": 44.15,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 11,
"guinier_point_last": 92,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEC9_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-13T15:54:20.401014+02:00",
"bragg_peak": []
}
