2. Measurements Reported by SASBDB Reported Results
Metric
Method
Value
Uncertainty
Unit
i0
Guinier
1.0
—
arbitrary
mw
Experimental
42.0
—
kDa
These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.
▼
3. Source Fits and Models Source Fits & Models
This entry has no source fit record.
▶
4. Source File Index Source Files
Category
Path
Download status
Size
curve
sasbdb/entries/w8/sasddw8/source/SASDDW8.dat
downloaded
7303
full_entry_zip
sasbdb/entries/w8/sasddw8/source/SASDDW8.zip
downloaded
1908
pddf
sasbdb/entries/w8/sasddw8/source/SASDDW8.out
not_listed
—
sascif
sasbdb/entries/w8/sasddw8/source/SASDDW8.sascif
downloaded
14082
summary
sasbdb/entries/w8/sasddw8/source/summary.json
downloaded
7295
▶
5. Experiment Description and Publication Experiment & Publication
Original Experiment Description
This data set displays SAXS data measured from the egg white from a Chinese century egg (pidan) prepared from quail eggs. The most abundant protein in the egg white is ovalbumin, but there are other proteins present. The pidan was prepared by soaking eggs in 0.9 M NaOH and 0.5 M NaCl for three weeks. The egg white formed a transparent gel during this process. The egg proteins experienced a partial unfolding and formed intermolecular cross-links. Because the proteins link to form extended materials, the parameter Rg and monomer molecular weight does not apply here. Similarly, because this is a measurement of intact biological tissue, there is no experimental buffer per se to subtract, and accordingly, raw data without buffer subtraction are reported here. The sample measurement (1 x 1800 s exposure) was performed at 10°C. Measurements used a rotating-anode system with Cu Kα radiation (λ = 0.1542 nm) from a Bruker-Nonius FR591 generator operated at 3.4 kW. Collimation was performed using circular pinholes and Osmic Max-Flux confocal optics. The scattered X-rays (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle) were collected using a Bruker Hi-Star area detector. Data were collected at sample−detector distances of 54 and 150 cm, and the data merged to create a single profile over the range q ∈ [0.08, 3.5] nm−1. To minimize background, an integral vacuum with a pressure of < 0.3 mbar was maintained along the entire flight path.
Related Publication
Title
The Proof Is in the <i>Pidan</i>: Generalizing Proteins as Patchy Particles.
Authors
Cai J, Sweeney AM
DOI / PMID
10.1021/acscentsci.8b00187 / 30062112
▼
6. Complete Source Record Complete Source Record
The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
This data set displays SAXS data measured from the egg white from a Chinese century egg (pidan) prepared from quail eggs. The most abundant protein in the egg white is ovalbumin, but there are other proteins present. The pidan was prepared by soaking eggs in 0.9 M NaOH and 0.5 M NaCl for three weeks. The egg white formed a transparent gel during this process. The egg proteins experienced a partial unfolding and formed intermolecular cross-links. Because the proteins link to form extended materials, the parameter Rg and monomer molecular weight does not apply here. Similarly, because this is a measurement of intact biological tissue, there is no experimental buffer per se to subtract, and accordingly, raw data without buffer subtraction are reported here. The sample measurement (1 x 1800 s exposure) was performed at 10°C. Measurements used a rotating-anode system with Cu Kα radiation (λ = 0.1542 nm) from a Bruker-Nonius FR591 generator operated at 3.4 kW. Collimation was performed using circular pinholes and Osmic Max-Flux confocal optics. The scattered X-rays (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle) were collected using a Bruker Hi-Star area detector. Data were collected at sample−detector distances of 54 and 150 cm, and the data merged to create a single profile over the range q ∈ [0.08, 3.5] nm−1. To minimize background, an integral vacuum with a pressure of < 0.3 mbar was maintained along the entire flight path.
{
"code": "SASDDW8",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "The Proof Is in the <i>Pidan</i>: Generalizing Proteins as Patchy Particles.",
"publication": {
"title": "The Proof Is in the <i>Pidan</i>: Generalizing Proteins as Patchy Particles.",
"author_list": "Cai J, Sweeney AM",
"journal": "ACS Cent Sci",
"doi": "10.1021/acscentsci.8b00187",
"pmid": "30062112",
"published_date": "2018 Jul 25"
},
"status": "released",
"submitted_date": "2018-06-23",
"released_date": "2018-07-20"
},
"pddf_data": null,
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDW8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDW8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDW8_kratky_img.png",
"pddf_plot": null,
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDW8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDW8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "multiwire",
"name": "Bruker HI-STAR",
"resolution": 0.0
},
"name": "University of Pennslyvania",
"city": "Philadelphia, PA",
"country": "USA",
"beamline_name": "Bruker Nonius FR591",
"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": "Ovalbumin (common quail)",
"short_name": "Ova",
"sequence": "GSIGAASMEFCFDVFKELKVHHANDNMLYSPFAILSTLAMVFLGAKDSTRTQINKVVHFDKLPGFGDSI\r\nEAQCGTSANVHSSLRDILNQITKQNDAYSFSLASRLYAQETYTVVPEYLQCVKELYRGGLESVNFQTAAD\r\nQARGLINAWVESQTNGIIRNILQPSSVDSQTAMVLVNAIAFKGLWEKAFKAEDTQTIPFRVTEQESKPVQ\r\nMMHQIGSFKVASMASEKMKILELPFASGTMSMLVLLPDDVSGLEQLESTISFEKLTEWTSSSIMEERKVK\r\nVYLPRMKMEEKYNLTSLLMAMGITDLFSSSANLSGISSVGSLKIPQAVHAAYAEINEAGRDVVGSAEAGV\r\nDATEEFRADHPFLFCVKHIETNAILLFGRCVSP",
"organism": "Coturnix coturnix",
"uniprot_code": "Q6V115",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MGSIGAASMEFCFDVFKELKVHHANDNMLYSPFAILSTLAMVFLGAKDSTRTQINKVVHF\nDKLPGFGDSIEAQCGTSANVHSSLRDILNQITKQNDAYSFSLASRLYAQETYTVVPEYLQ\nCVKELYRGGLESVNFQTAADQARGLINAWVESQTNGIIRNILQPSSVDSQTAMVLVNAIA\nFKGLWEKAFKAEDTQTIPFRVTEQESKPVQMMHQIGSFKVASMASEKMKILELPFASGTM\nSMLVLLPDDVSGLEQLESTISFEKLTEWTSSSIMEERKVKVYLPRMKMEEKYNLTSLLMA\nMGITDLFSSSANLSGISSVGSLKIPQAVHAAYAEINEAGRDVVGSAEAGVDATEEFRADH\nPFLFCVKHIETNAILLFGRCVSP",
"mw": 42.078,
"total_mw": 42.078,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "Water",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Chinese century egg albumen (pidan) made from quail egg",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "Penn",
"address": "Philadelphia, PA, United States",
"full_name": "University of Pennsylvania",
"webpage": "http://www.upenn.edu/"
}
],
"contributor_name": "Jing",
"contributor_surname": "Cai",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-06-27",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 1800.0,
"number_of_frames": 1,
"wavelength": 0.1542,
"sample_detector_distance": 1.5,
"concentration_min": null,
"concentration_max": 170.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.08,
"s_max": 3.28,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [],
"estimated_volume_method": null,
"pddf_software": null,
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "This data set displays SAXS data measured from the egg white from a Chinese century egg (pidan) prepared from quail eggs. The most abundant protein in the egg white is ovalbumin, but there are other proteins present. The pidan was prepared by soaking eggs in 0.9 M NaOH and 0.5 M NaCl for three weeks. The egg white formed a transparent gel during this process. The egg proteins experienced a partial unfolding and formed intermolecular cross-links. Because the proteins link to form extended materials, the parameter Rg and monomer molecular weight does not apply here. Similarly, because this is a measurement of intact biological tissue, there is no experimental buffer per se to subtract, and accordingly, raw data without buffer subtraction are reported here. The sample measurement (1 x 1800 s exposure) was performed at 10°C. Measurements used a rotating-anode system with Cu Kα radiation (λ = 0.1542 nm) from a Bruker-Nonius FR591 generator operated at 3.4 kW. Collimation was performed using circular pinholes and Osmic Max-Flux confocal optics. The scattered X-rays (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle) were collected using a Bruker Hi-Star area detector. Data were collected at sample−detector distances of 54 and 150 cm, and the data merged to create a single profile over the range q ∈ [0.08, 3.5] nm−1. To minimize background, an integral vacuum with a pressure of < 0.3 mbar was maintained along the entire flight path.",
"tags": [
"softmatter"
],
"intensity_unit": "arbitrary",
"experimental_mw": 42.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": null,
"pddf_i0_error": null,
"guinier_i0": 1.0,
"guinier_i0_error": null,
"pddf_rg": null,
"pddf_rg_error": null,
"guinier_rg": null,
"guinier_rg_error": null,
"pddf_dmax": null,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": null,
"guinier_point_last": null,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDW8_datloglog_img.png",
"symmetry": null,
"last_modified": "2022-01-27T08:14:23.545135+01:00",
"bragg_peak": []
}
