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": "SASDCZ2",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Structure and dynamics of the RNAPII CTDsome with Rtt103.",
"publication": {
"title": "Structure and dynamics of the RNAPII CTDsome with Rtt103.",
"author_list": "Jasnovidova O, Klumpler T, Kubicek K, Kalynych S, Plevka P, Stefl R",
"journal": "Proc Natl Acad Sci U S A",
"doi": "10.1073/pnas.1712450114",
"pmid": "29073019",
"published_date": "2017 Oct 17"
},
"status": "released",
"submitted_date": "2017-04-19",
"released_date": "2017-10-12"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCZ2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCZ2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCZ2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCZ2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCZ2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCZ2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCZ2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 100K",
"resolution": 172.0
},
"name": "CEITEC",
"city": "Brno",
"country": "Czech Republic",
"beamline_name": "Rigaku BioSAXS-1000",
"beam_geometry": "",
"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": "Regulator of Ty1 transposition protein 103",
"short_name": null,
"sequence": "MPFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLG\r\nLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFS\r\nKQVVNDIERSLKTESSPVEALVLPQKLKDFAKDYEKLVKMHHNVCAMKMRFDKSSDELDP\r\nSSSVYEENFKTISKIGNMAKDIINESILKRESGIHKLQSTLDDEKRHLDEEQNMLSEIEF\r\nVLSAKDL",
"organism": "Saccharomyces cerevisiae",
"uniprot_code": "Q05543",
"uniprot_range_first": 1,
"uniprot_range_last": 246,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MPFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLG\nLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFS\nKQVVNDIERSLKTESSPVEALVLPQKLKDFAKDYEKLVKMHHNVCAMKMRFDKSSDELDP\nSSSVYEENFKTISKIGNMAKDIINESILKRESGIHKLQSTLDDEKRHLDEEQNMLSEIEF\nVLSAKDPSRLNKNVDEDNIIPTYEVGDGDDDDDDGDNDDDDDDDDDDKNYDDRSNDSNYG\nVTNISTTDKKNEVVEKTDSEHKNSTHNPSDNQFGMKRTHDMIGHDDANDIPEKKVHLDSK\nTSEDGTFNSEDGHYELDIEGHVGAQTDEGVENSGGVSSSIQDLLSKLAN",
"mw": 28.627,
"total_mw": 57.254,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
},
{
"long_name": "DNA-directed RNA polymerase II subunit RPB1",
"short_name": null,
"sequence": "SPEFTCEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPTSPSYEPAAADYKDDDDK",
"organism": "Saccharomyces cerevisiae",
"uniprot_code": "P04050",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS\nIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE\nLMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK\nLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP\nVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV\nATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE\nLDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR\nAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA\nDFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF\nIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP\nKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN\nGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR\nFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV\nDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR\nLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD\nLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI\nRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC\nLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT\nLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH\nTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA\nAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML\nKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP\nGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG\nLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA\nFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS\nNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS\nPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS\nPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP\nSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR",
"mw": 12.782,
"total_mw": 12.782,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM KH2PO4, 300 mM KCl, 10 mM BME",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.5,
"deuteration": null
},
"purity_method": null,
"name": "Yeast CTDsome: transcription termination factor Rtt103p/C-terminal domain of DNA-directed RNA polymerase II subunit RPB1 (Rtt103 1-246-phospho-mimetic complex)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "CEITEC - Central European Institute of Technology, Masaryk University",
"webpage": "https://www.ceitec.eu/"
}
],
"contributor_name": "Tomas",
"contributor_surname": "Klumpler",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-04-12",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 3600.0,
"number_of_frames": 5,
"wavelength": 0.154,
"sample_detector_distance": 0.4806,
"concentration_min": null,
"concentration_max": 1.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.037,
"s_max": 6.627,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCZ2_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "5m48",
"ext_code": "5M48",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "05",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCZ2_fit1_model1.pdb",
"model_mw": 189.4,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/coral3.log",
"symmetry": "",
"comment": "",
"user": 195
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCZ2_fit1_fit_img.png",
"software": "CORAL",
"chi_square_value": 0.79,
"p_value": 0.5455,
"fit_residual_plot": "SASDCZ2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCZ2_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coral3.log",
"software_version": "05",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCZ2_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": "05",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCZ2_fit2_model1.pdb",
"model_mw": 189.4,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/coral2_model.log",
"symmetry": "",
"comment": "",
"user": 195
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCZ2_fit2_fit_img.png",
"software": "CORAL",
"chi_square_value": 0.81,
"p_value": 0.9664,
"fit_residual_plot": "SASDCZ2_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCZ2_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coral2_LEL9vvf.log",
"software_version": "05",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCZ2_fit3_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "5m48",
"ext_code": "5M48",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "05",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCZ2_fit3_model1.pdb",
"model_mw": 189.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "",
"comment": "",
"user": 195
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCZ2_fit3_fit_img.png",
"software": "CORAL",
"chi_square_value": 0.81,
"p_value": 0.321,
"fit_residual_plot": "SASDCZ2_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCZ2_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coral1_C5oeQKy.log",
"software_version": "05",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "SAXS data from solutions of Rtt103 1-246-phospho-mimetic complex in 25 mM KH2PO4, 300 mM KCl, 10 mM β-mercaptoethanol, pH 6.5 were collected using a BioSAXS-1000 instrument at CEITEC (Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Five successive 3600 second frames were collected at a sample temperature of 4°C. The data were normalized to the intensity of the transmitted beam and radially averaged and the corresponding scattering from the solvent-blank was subtracted to produce the scattering profile displayed in this entry.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 184.5,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 350.625,
"porod_mw_error": null,
"pddf_i0": 0.1937,
"pddf_i0_error": 0.00423,
"guinier_i0": 0.18,
"guinier_i0_error": 0.0027,
"pddf_rg": 5.767,
"pddf_rg_error": 0.014,
"guinier_rg": 5.294,
"guinier_rg_error": 0.02,
"pddf_dmax": 21.0,
"pddf_dmax_error": null,
"porod_volume": 561.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 7,
"guinier_point_last": 15,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCZ2_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-06-01T08:36:00.956593+02:00",
"bragg_peak": []
}
