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": "SASDB86",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "Potent and selective bivalent inhibitors of BET bromodomains.",
"publication": {
"title": "Potent and selective bivalent inhibitors of BET bromodomains.",
"author_list": "Waring MJ, Chen H, Rabow AA, Walker G, Bobby R, Boiko S, Bradbury RH, Callis R, Clark E, Dale I, Daniels DL, Dulak A, Flavell L, Holdgate G, Jowitt TA, Kikhney A, McAlister M, Méndez J, Ogg D, Patel J, Petteruti P, Robb GR, Robers MB, Saif S, Stratton N, Svergun DI, Wang W, Whittaker D, Wilson DM, Yao Y",
"journal": "Nat Chem Biol",
"doi": "10.1038/nchembio.2210",
"pmid": "27775716",
"published_date": "2016 Dec"
},
"status": "released",
"submitted_date": "2016-09-02",
"released_date": "2016-10-26"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB86.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB86.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB86_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB86_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB86_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB86_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB86.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": "Bromodomain-containing protein 4",
"short_name": "BRD4",
"sequence": "MAHHHHHHSSGVDLGTENLYFQSMMSAESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAA\r\nSMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWN\r\nAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE\r\nTEIMIVQAKGRGRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMTVVPPQPLQ\r\nTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTIDPIHEPPSLPPEPKTTKLGQRRESSRPV\r\nKPPKKDVPDSQQHPAPEKSS\r\nKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSN\r\nCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD\r\nEPEEPVVAVSSPAVPPPT",
"organism": "Homo sapiens",
"uniprot_code": "O60885",
"uniprot_range_first": 1,
"uniprot_range_last": 477,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSAESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAASTNPPPPETSNPNKPKRQT\nNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYW\nNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRG\nRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMT\nVVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTI\nDPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQHPAPEKSSKVSEQLKCCSGI\nLKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGA\nDVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVAVSSPAVPPPTKVV\nAPPSSSDSSSDSSSDSDSSTDDSEEERAQRLAELQEQLKAVHEQLAALSQPQQNKPKKKE\nKDKKEKKKEKHKRKEEVEENKKSKAKEPPPKKTKKNNSSNSNVSKKEPAPMKSKPPPTYE\nSEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLK\nPSTLRELERYVTSCLRKKRKPQAEKVDVIAGSSKMKGFSSSESESSSESSSSDSEDSETE\nMAPKSKKKGHPGREQKKHHHHHHQQMQQAPAPVPQQPPPPPQQPPPPPPPQQQQQPPPPP\nPPPSMPQQAAPAMKSSPPPFIATQVPVLEPQLPGSVFDPIGHFTQPILHLPQPELPPHLP\nQPPEHSTPPHLNQHAVVSPPALHNALPQQPSRPSNRAAALPPKPARPPAVSPALTQTPLL\nPQPPMAQPPQVLLEDEEPPAPPLTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPLPP\nPPHPSVQQQLQQQPPPPPPPQPQPPPQQQHQPPPRPVHLQPMQFSTHIQQPPPPQGQQPP\nHPPPGQQPPPPQPAKPQQVIQHHHSPRHHKSDPYSTGHLREAPSPLMIHSPQMSQFQSLT\nHQSPPQQNVQPKKQELRAASVVQPQPLVVVKEEKIHSPIIRSEPFSPSLRPEPPKHPESI\nKAPVHLPQRPEMKPVDVGRPVIRPPEQNAPPPGAPDKDKQKQEPKTPVAPKKDLKIKNMG\nSWASLVQKHPTTPSSTAKSSSDSFEQFRRAAREKEEREKALKAQAEHAEKEKERLRQERM\nRSREDEDALEQARRAHEEARRRQEQQQQQRQEQQQQQQQQAAAVAAAATPQAQSSQPQSM\nLDQQRELARKREQERRRREAMAATIDMNFQSDLLSIFEENLF",
"mw": 55.836,
"total_mw": 55.836,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20mM Hepes, 100mM NaCl, 1mM Tris(2-carboxyethyl)phosphine hydrochloride",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "apo-BRD4",
"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": "Al",
"contributor_surname": "Kikhney",
"orcid": "https://orcid.org/0000-0003-1321-3956"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2014-09-12",
"storage_temperature": null,
"cell_temperature": null,
"exposure_time": 0.2,
"number_of_frames": 50,
"wavelength": 0.09919,
"sample_detector_distance": 2.87,
"concentration_min": 1.0,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.036,
"s_max": 4.969,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB86_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r4311",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDB86_fit1_model1.pdb",
"model_mw": 94.0,
"bead_radius": 5.7,
"log": "https://www.sasbdb.org/media/log_files/apo_zc1u_7_3Bs6FK8.log",
"symmetry": "",
"comment": "",
"user": 4
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB86_fit1_fit_img.png",
"software": null,
"chi_square_value": 6.718464,
"p_value": 0.013168,
"fit_residual_plot": "SASDB86_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB86_fit1.fir",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB86_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [
{
"pdb_code": "2oss",
"ext_code": "2oss",
"ext_type": "pdb",
"difference_with_model": "derived"
},
{
"pdb_code": "2yem",
"ext_code": "2yem",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDB86_fit2_model1.pdb",
"model_mw": 56.75,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 4
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB86_fit2_fit_img.png",
"software": null,
"chi_square_value": 9.591409,
"p_value": 0.0,
"fit_residual_plot": "SASDB86_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB86_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM 4.6",
"i0_calibration_standard": null,
"description": "A pool of 10000 models comprising two rigid bromodomains (residues 42-168, PDB ID: 2oss and 349-458, PDB ID: 2yem) connected by a flexible linker, N-terminal tag and flexible N- and C-termini were generated by the program RANCH (EOM). The scattering from each model from the pool was calculated with the program CRYSOL. For the 100 models best fitting the experimental scattering the histograms of the distances between the centres of the two bromodomains were computed; the average distance was 14±1 nm, the average Rg was 7.2±0.5 nm.",
"experiment_description": null,
"tags": [],
"intensity_unit": null,
"experimental_mw": 37.2,
"experimental_mw_error": null,
"guinier_i0_mw": 37.2,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 48.77,
"pddf_i0_error": null,
"guinier_i0": 48.2,
"guinier_i0_error": null,
"pddf_rg": 7.37,
"pddf_rg_error": null,
"guinier_rg": 6.99,
"guinier_rg_error": 0.3,
"pddf_dmax": 27.0,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 8,
"guinier_point_last": 25,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDB86_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
