The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDBM4",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system.",
"publication": {
"title": "Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system.",
"author_list": "Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L",
"journal": "Nucleic Acids Res",
"doi": "10.1093/nar/gkw469",
"pmid": "27216815",
"published_date": "2016 Jul 8"
},
"status": "released",
"submitted_date": "2016-03-18",
"released_date": "2016-09-01"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBM4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBM4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBM4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBM4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBM4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBM4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBM4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"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": "Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family)",
"short_name": "Cas6f",
"sequence": "MNSYIDIRLKPDAEMREAELSSKVFTKFHKALVTLNSHKIGISFPQMKLSLGQLFRIHGDASLLHDLQGLDWLGPLAGYCQVTAVSAVPDHVQYRIVSVKRSNLSKAKLKRLIARGSIDKDGEKRYKVKMLGQGFDNPYLDLFSSSTGQVYRKFFEFSDIQAHPLDGEFDSYGLSKTATVPWF",
"organism": "Shewanella putrefaciens",
"uniprot_code": "A4Y6G3",
"uniprot_range_first": 1,
"uniprot_range_last": 183,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MNSYIDIRLKPDAEMREAELSSKVFTKFHKALVTLNSHKIGISFPQMKLSLGQLFRIHGD\nASLLHDLQGLDWLGPLAGYCQVTAVSAVPDHVQYRIVSVKRSNLSKAKLKRLIARGSIDK\nDGEKRYKVKMLGQGFDNPYLDLFSSSTGQVYRKFFEFSDIQAHPLDGEFDSYGLSKTATV\nPWF",
"mw": 20.674,
"total_mw": 20.674,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822)",
"short_name": "Cas5fv",
"sequence": "MKIIIEYDSCWRNAFLGGSNNEPVPKKGREFLGSMTSLKKEGNFKVCENTLDTVMGVLNRLIGDQRKLYQARSKMYESAYYFEALEDKVSFIDKPQLTNEISFIRNMNGSTDQNAFTGMIKVSDPVFTSEYSQQFWGVLALDFTQLCDFIIKQSQVVGSIELNPLSIINRLESLNQEKALENSDDLAQVLKVLNEYFPDIEYLNNKGLITPISIYCSALYLQLARLETSFNMTTAKTKAGGISGISKRGFTKKDFMDRYTTGPKKTIWGNPFIKKEKIKGQGEVTSMMTKASGQLEISIDVDRDKAQEIKILIENAGVSSFYLGKKGLAYVSNIKL",
"organism": "Shewanella putrefaciens",
"uniprot_code": "A4Y6G2",
"uniprot_range_first": 1,
"uniprot_range_last": 336,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKIIIEYDSCWRNAFLGGSNNEPVPKKGREFLGSMTSLKKEGNFKVCENTLDTVMGVLNR\nLIGDQRKLYQARSKMYESAYYFEALEDKVSFIDKPQLTNEISFIRNMNGSTDQNAFTGMI\nKVSDPVFTSEYSQQFWGVLALDFTQLCDFIIKQSQVVGSIELNPLSIINRLESLNQEKAL\nENSDDLAQVLKVLNEYFPDIEYLNNKGLITPISIYCSALYLQLARLETSFNMTTAKTKAG\nGISGISKRGFTKKDFMDRYTTGPKKTIWGNPFIKKEKIKGQGEVTSMMTKASGQLEISID\nVDRDKAQEIKILIENAGVSSFYLGKKGLAYVSNIKL",
"mw": 37.861,
"total_mw": 37.861,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Nonameric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821)",
"short_name": "Cas7fv-nonamer",
"sequence": "MGSSHHHHHHSQNPMQKVTGIKSVDFKIKALGHGVVNWNGPTTLTGDDGKTVDNHTLPKLRGYTNLTGKVKDETGYKYKKQATDINFKETPLYISQNCIRHHLFREQAFDLHYASDKNLKNVLASITGLIRGYVVPSSQCKRTSPLLLEDFVDQLGNGNFEQYGQAGARDSTSFFSKTTFGDTEYISYGSISIEQLQFISLDKKFDRAAMVIKEGEGEVIAAELQNYIQSLNPSLNPQAIFHSNYVRRGTIFEEGECGILLNDDAVKALVAETLERLANLSIRQAKGYMYVDDITVDYNDSHKMMRIKRDESEIINEQHAPFAQYFYAK\r\n",
"organism": "Shewanella putrefaciens",
"uniprot_code": "A4Y6G1",
"uniprot_range_first": 1,
"uniprot_range_last": 315,
"oligomerization": "nonamer",
"molecular_type": "protein",
"uniprot_sequence": "MQKVTGIKSVDFKIKALGHGVVNWNGPTTLTGDDGKTVDNHTLPKLRGYTNLTGKVKDET\nGYKYKKQATDINFKETPLYISQNCIRHHLFREQAFDLHYASDKNLKNVLASITGLIRGYV\nVPSSQCKRTSPLLLEDFVDQLGNGNFEQYGQAGARDSTSFFSKTTFGDTEYISYGSISIE\nQLQFISLDKKFDRAAMVIKEGEGEVIAAELQNYIQSLNPSLNPQAIFHSNYVRRGTIFEE\nGECGILLNDDAVKALVAETLERLANLSIRQAKGYMYVDDITVDYNDSHKMMRIKRDESEI\nINEQHAPFAQYFYAK",
"mw": 37.168,
"total_mw": 334.515,
"number_molecules": 9,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "long-crRNA: CRISPR/Cas Type I-F Cascade component",
"short_name": "long-crRNA",
"sequence": "CUUAGAAACGCUAAUGCACUCAAUCCUAUCGCCCAGCAAGACGCGCAAACCUAUAACCGUUCACCGCCGCACAGGCGG",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "RNA",
"uniprot_sequence": null,
"mw": 24.987,
"total_mw": 24.987,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES 150 mM NaCl 1mM DTT 1mM EDTA",
"concentration_unit": "mM",
"comment": null,
"additive": "150 mM NaCl, 1mM DTT, 1mM EDTA",
"concentration": 50.0,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "The 1:1:9:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F long Cascade complex",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Marburg, Germany",
"full_name": "University of Marburg",
"webpage": "http://www.uni-marburg.de/"
}
],
"contributor_name": "Patrick",
"contributor_surname": "Pausch",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": "mg/ml",
"date": "2016-01-30",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.93,
"sample_detector_distance": 2.43,
"concentration_min": null,
"concentration_max": 25.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.033,
"s_max": 4.945,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBM4_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/SASDBM4_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 4.5,
"log": null,
"symmetry": "",
"comment": "",
"user": 118
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBM4_fit1_fit_img.png",
"software": null,
"chi_square_value": 3.5,
"p_value": 0.0,
"fit_residual_plot": "SASDBM4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBM4_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBM4_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBM4_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 6.0,
"log": null,
"symmetry": "",
"comment": "",
"user": 118
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBM4_fit2_fit_img.png",
"software": null,
"chi_square_value": 4.5,
"p_value": 0.0,
"fit_residual_plot": "SASDBM4_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBM4_fit2.fir",
"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": null,
"experiment_description": "Synchrotron SAXS data from solutions of the 1:1:9:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F Cascade complex in 50 mM HEPES 150 mM NaCl, 1mM DTT, 1mM EDTA, pH 7 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). The data displayed in this entry were measured from one sample at a solute concentration of 25 mg/ml using an exposure time of 10 s (collected as 10 x 1 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data were normalized to protein concentration. ",
"tags": [],
"intensity_unit": null,
"experimental_mw": 324.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 86.7,
"pddf_i0_error": 0.04,
"guinier_i0": 87.3,
"guinier_i0_error": 0.12,
"pddf_rg": 6.52,
"pddf_rg_error": 0.003,
"guinier_rg": 6.5,
"guinier_rg_error": 0.23,
"pddf_dmax": 21.6,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 20,
"guinier_point_last": 34,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBM4_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
