SASDFM6

Adenine specific DNA methyltransferase (Mod HP_0593) at pH 5.5

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2019-12-06T13:07:15.624532+01:00

The sample is severely aggregated. Wavelength UNKNOWN; Experimental temperature, UNKNOWN; Exposure time, UNKNOWN; Sample to detector distance, UNKNOWN.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Adenine specific DNA methyltransferase (Mod HP_0593) at pH 5.5

浓度— – 2.0 缓冲液 / pH25 mM citrate, 250 mM NaCl / 5.5
实验温度— 设备 / 束线ESRF / BM29
波长— nm曝光— s × —

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Adenine specific DNA methyltransferase (Mod)
查看序列
MLLKNFPQTIKDGQVSLSAIKMLLGFNESMNDISGYELTWTGKGFANALYSEPCQKQLKLQESFTPQTSASKHPNNAIIIGDNLDALKLLKSAYSEKIKMIYIDPPYNTGNDEFIYPDNFRQDYQKILREVGLMEIDENGKEIESESLKFFKNTQGSGTHSGWLSFMLPRLKLARDLLKEDGVIFISIDDNECANLKILCDEIFGEDNFVGDFIRKTKSTTNDAKIGLNYQHEFLLCYAKDKNYTNLLGGEKNLENYKNPDNDPNGAWINDNPSAKSGNMKTGYFGVTNPYTNKVDYPPVGMFWRFSQNTIQKHIDEGRICFKKEHKDNERGFIYKRYLKDLKTTQKTFDSLIFSDNCYMNQAATKELLNLGMGEYFTYPKGVEFMKKIILHSTTPNEGDIILDFFAGSGTTVHAVMELNAEDKGNREFILVQIDEEIKEDESAYDFCKKELKSAKPVISDITIERVKRAAQKISQLSKDSGLDLGFKVYTLQDKVQIINDKEEITLFNRSDLTPFDKALNLALQCGKTLNQALEIIIKDKLYKCEDAYFCIVCDEEAQEYLAKSKNEMIFLDGYEEIDLEAFLNLNASFKERLSVVY
proteinHelicobacter pyloriO253151–598tetramer分子数 468.367 kDa

实验曲线

曲线点数 / 列q 范围误差质量负强度点来源文件
11043[3]0.03750981–4.946231 1/nm含误差列缺失 0156sasbdb/entries/m6/sasdfm6/source/SASDFM6.dat
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2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)19.1—nm
i0Guinier126.760.8arbitrary
i0P(r)122.9—arbitrary
mwExperimental250.0—kDa
mwPorod209.0—kDa
porod_volumePorod316.0—nm³
rgGuinier4.980.42nm
rgP(r)4.91—nm

这些数值是 SASBDB 来源记录,不是 SAXSdb 对实验曲线重新计算的结果。

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3. 来源拟合与模型 Source Fits & Models

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4. 来源文件索引 Source Files

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5. 实验说明与论文 Experiment & Publication

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6. 完整来源记录 Complete Source Record

下列内容直接来自 SASBDB 条目。字段没有值时显示“—”;未声明的单位不会由 SAXSdb 猜测。

打开 SASBDB 原始条目

缓冲液与样品属性

缓冲液名称25 mM citrate, 250 mM NaCl缓冲液浓度—
pH5.5添加剂—
缓冲液说明—
纯度测定方法—消光系数—
吸收值—散射对比度—
比体积 / 干体积— / —混合物 / 氘代— / —

采集条件与仪器

测量日期2018-12-01储存 / 测量温度— / —
曝光时间—帧数—
波长—样品-探测器距离—
光源X-ray synchrotron探测器Pilatus 1M
机构 / 束线ESRF / BM29 · Grenoble, France
q 范围0.038 – 4.946样品体积 / 流速— / —

SASBDB 原始图

实验 I(q)
实验 I(q)
实验 I(q) log-log
实验 I(q) log-log
Guinier 图
Guinier 图
Kratky 图
Kratky 图
P(r) 图
P(r) 图

可下载文件

类别文件状态大小校验值下载与查看
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full_entry_zipsasbdb/entries/m6/sasdfm6/source/SASDFM6.zipdownloaded5341533b7e8493508d470665068d64d81bb600ff6453570ef51a309385003030836aeb下载查看原文件源站
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curve:来源记录
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full_entry_zip:来源记录与 ZIP 内部目录(4 项)
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pddf:来源记录
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sascif:来源记录
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summary:来源记录
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全部来源字段(无筛选)

这里自动展开来源记录中的每一个字段,包括空值、列表成员和页面上方已展示过的字段。

summary.json:156 个字段值
字段路径原始值
codeSASDFM6
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleTetramerization at low pH licenses DNA methylation activity of M.HpyAXI in the presence of acid stress.
project.publication.titleTetramerization at low pH licenses DNA methylation activity of M.HpyAXI in the presence of acid stress.
project.publication.author_listNarayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2019.10.001
project.publication.pmid31628946
project.publication.published_date2019 Oct 16
project.statusreleased
project.submitted_date2019-05-31
project.released_date2019-11-17
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDFM6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDFM6.dat
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFM6_pofr_img.png
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFM6.sascif
experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameAdenine specific DNA methyltransferase (Mod)
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMLLKNFPQTIKDGQVSLSAIKMLLGFNESMNDISGYELTWTGKGFANALYSEPCQKQLKL QESFTPQTSASKHPNNAIIIGDNLDALKLLKSAYSEKIKMIYIDPPYNTGNDEFIYPDNF RQDYQKILREVGLMEIDENGKEIESESLKFFKNTQGSGTHSGWLSFMLPRLKLARDLLKE DGVIFISIDDNECANLKILCDEIFGEDNFVGDFIRKTKSTTNDAKIGLNYQHEFLLCYAK DKNYTNLLGGEKNLENYKNPDNDPNGAWINDNPSAKSGNMKTGYFGVTNPYTNKVDYPPV GMFWRFSQNTIQKHIDEGRICFKKEHKDNERGFIYKRYLKDLKTTQKTFDSLIFSDNCYM NQAATKELLNLGMGEYFTYPKGVEFMKKIILHSTTPNEGDIILDFFAGSGTTVHAVMELN AEDKGNREFILVQIDEEIKEDESAYDFCKKELKSAKPVISDITIERVKRAAQKISQLSKD SGLDLGFKVYTLQDKVQIINDKEEITLFNRSDLTPFDKALNLALQCGKTLNQALEIIIKD KLYKCEDAYFCIVCDEEAQEYLAKSKNEMIFLDGYEEIDLEAFLNLNASFKERLSVVY
experiment.sample.molecule[0].organismHelicobacter pylori
experiment.sample.molecule[0].uniprot_codeO25315
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last598
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMLLKNFPQTIKDGQVSLSAIKMLLGFNESMNDISGYELTWTGKGFANALYSEPCQKQLKL QESFTPQTSASKHPNNAIIIGDNLDALKLLKSAYSEKIKMIYIDPPYNTGNDEFIYPDNF RQDYQKILREVGLMEIDENGKEIESESLKFFKNTQGSGTHSGWLSFMLPRLKLARDLLKE DGVIFISIDDNECANLKILCDEIFGEDNFVGDFIRKTKSTTNDAKIGLNYQHEFLLCYAK DKNYTNLLGGEKNLENYKNPDNDPNGAWINDNPSAKSGNMKTGYFGVTNPYTNKVDYPPV GMFWRFSQNTIQKHIDEGRICFKKEHKDNERGFIYKRYLKDLKTTQKTFDSLIFSDNCYM NQAATKELLNLGMGEYFTYPKGVEFMKKIILHSTTPNEGDIILDFFAGSGTTVHAVMELN AEDKGNREFILVQIDEEIKEDESAYDFCKKELKSAKPVISDITIERVKRAAQKISQLSKD SGLDLGFKVYTLQDKVQIINDKEEITLFNRSDLTPFDKALNLALQCGKTLNQALEIIIKD KLYKCEDAYFCIVCDEEAQEYLAKSKNEMIFLDGYEEIDLEAFLNLNASFKERLSVVY
experiment.sample.molecule[0].mw68.367
experiment.sample.molecule[0].total_mw273.468
experiment.sample.molecule[0].number_molecules4
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name25 mM citrate, 250 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph5.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameAdenine specific DNA methyltransferase (Mod HP_0593) at pH 5.5
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_nameRCB
experiment.contributor[0].affiliation[0].addressHaryana, India
experiment.contributor[0].affiliation[0].full_nameRegional Centre for Biotechnology
experiment.contributor[0].affiliation[0].webpagehttp://www.rcb.res.in/
experiment.contributor[0].contributor_nameNaveen
experiment.contributor[0].contributor_surnameNarayanan
experiment.contributor[0].orcidhttps://orcid.org/0000-0001-8327-1559
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-12-01
experiment.storage_temperaturenull
experiment.cell_temperaturenull
experiment.exposure_timenull
experiment.number_of_framesnull
experiment.wavelengthnull
experiment.sample_detector_distancenull
experiment.concentration_minnull
experiment.concentration_max2.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.038
experiment.s_max4.946
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFM6_fit1_model1_img.png
fits[0].models[0].softwarePyMOL
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
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fits[0].models[0].model_mw233.8
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user451
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value1.796
fits[0].p_value0.0
fits[0].fit_residual_plottetramer_after_md00_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDFM6_fit1.fit
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionThe sample is severely aggregated. Wavelength UNKNOWN; Experimental temperature, UNKNOWN; Exposure time, UNKNOWN; Sample to detector distance, UNKNOWN.
experiment_descriptionSynchrotron SAXS data from solutions of adenine specific DNA methyltransferase (Mod HP_0593) at pH 5.5 in 25 mM citrate, 250 mM NaCl were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw250.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw209.0
porod_mw_errornull
pddf_i0122.9
pddf_i0_errornull
guinier_i0126.76
guinier_i0_error0.8
pddf_rg4.91
pddf_rg_errornull
guinier_rg4.98
guinier_rg_error0.42
pddf_dmax19.1
pddf_dmax_errornull
porod_volume316.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first18
guinier_point_last47
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFM6_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDFM6
statussuccess
started_at2026-08-11T15:12:28.105945+00:00
finished_at2026-08-11T15:12:40.244100+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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查看完整 summary.json 原文
{
  "code": "SASDFM6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Tetramerization at low pH licenses DNA methylation activity of M.HpyAXI in the presence of acid stress.",
    "publication": {
      "title": "Tetramerization at low pH licenses DNA methylation activity of M.HpyAXI in the presence of acid stress.",
      "author_list": "Narayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2019.10.001",
      "pmid": "31628946",
      "published_date": "2019 Oct 16"
    },
    "status": "released",
    "submitted_date": "2019-05-31",
    "released_date": "2019-11-17"
  },
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        "resolution": 172.0
      },
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      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
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          "long_name": "Adenine specific DNA methyltransferase (Mod)",
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          "sequence": "MLLKNFPQTIKDGQVSLSAIKMLLGFNESMNDISGYELTWTGKGFANALYSEPCQKQLKL\r\nQESFTPQTSASKHPNNAIIIGDNLDALKLLKSAYSEKIKMIYIDPPYNTGNDEFIYPDNF\r\nRQDYQKILREVGLMEIDENGKEIESESLKFFKNTQGSGTHSGWLSFMLPRLKLARDLLKE\r\nDGVIFISIDDNECANLKILCDEIFGEDNFVGDFIRKTKSTTNDAKIGLNYQHEFLLCYAK\r\nDKNYTNLLGGEKNLENYKNPDNDPNGAWINDNPSAKSGNMKTGYFGVTNPYTNKVDYPPV\r\nGMFWRFSQNTIQKHIDEGRICFKKEHKDNERGFIYKRYLKDLKTTQKTFDSLIFSDNCYM\r\nNQAATKELLNLGMGEYFTYPKGVEFMKKIILHSTTPNEGDIILDFFAGSGTTVHAVMELN\r\nAEDKGNREFILVQIDEEIKEDESAYDFCKKELKSAKPVISDITIERVKRAAQKISQLSKD\r\nSGLDLGFKVYTLQDKVQIINDKEEITLFNRSDLTPFDKALNLALQCGKTLNQALEIIIKD\r\nKLYKCEDAYFCIVCDEEAQEYLAKSKNEMIFLDGYEEIDLEAFLNLNASFKERLSVVY",
          "organism": "Helicobacter pylori",
          "uniprot_code": "O25315",
          "uniprot_range_first": 1,
          "uniprot_range_last": 598,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "MLLKNFPQTIKDGQVSLSAIKMLLGFNESMNDISGYELTWTGKGFANALYSEPCQKQLKL\nQESFTPQTSASKHPNNAIIIGDNLDALKLLKSAYSEKIKMIYIDPPYNTGNDEFIYPDNF\nRQDYQKILREVGLMEIDENGKEIESESLKFFKNTQGSGTHSGWLSFMLPRLKLARDLLKE\nDGVIFISIDDNECANLKILCDEIFGEDNFVGDFIRKTKSTTNDAKIGLNYQHEFLLCYAK\nDKNYTNLLGGEKNLENYKNPDNDPNGAWINDNPSAKSGNMKTGYFGVTNPYTNKVDYPPV\nGMFWRFSQNTIQKHIDEGRICFKKEHKDNERGFIYKRYLKDLKTTQKTFDSLIFSDNCYM\nNQAATKELLNLGMGEYFTYPKGVEFMKKIILHSTTPNEGDIILDFFAGSGTTVHAVMELN\nAEDKGNREFILVQIDEEIKEDESAYDFCKKELKSAKPVISDITIERVKRAAQKISQLSKD\nSGLDLGFKVYTLQDKVQIINDKEEITLFNRSDLTPFDKALNLALQCGKTLNQALEIIIKD\nKLYKCEDAYFCIVCDEEAQEYLAKSKNEMIFLDGYEEIDLEAFLNLNASFKERLSVVY",
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          "number_molecules": 4,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "25 mM citrate, 250 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 5.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Adenine specific DNA methyltransferase (Mod HP_0593) at pH 5.5",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "RCB",
            "address": "Haryana, India",
            "full_name": "Regional Centre for Biotechnology",
            "webpage": "http://www.rcb.res.in/"
          }
        ],
        "contributor_name": "Naveen",
        "contributor_surname": "Narayanan",
        "orcid": "https://orcid.org/0000-0001-8327-1559"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2018-12-01",
    "storage_temperature": null,
    "cell_temperature": null,
    "exposure_time": null,
    "number_of_frames": null,
    "wavelength": null,
    "sample_detector_distance": null,
    "concentration_min": null,
    "concentration_max": 2.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.038,
    "s_max": 4.946,
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    "seccolumn": null
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    {
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFM6_fit1_model1_img.png",
          "software": "PyMOL",
          "pdb_link": [],
          "model_title": null,
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          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFM6_fit1_model1.pdb",
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          "bead_radius": null,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 451
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      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/tetramer_after_md00_fixed_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 1.796,
      "p_value": 0.0,
      "fit_residual_plot": "tetramer_after_md00_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFM6_fit1.fit",
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      "description": ""
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  "i0_calibration_standard": null,
  "description": "The sample is severely aggregated. Wavelength UNKNOWN; Experimental temperature, UNKNOWN; Exposure time, UNKNOWN; Sample to detector distance, UNKNOWN.",
  "experiment_description": "Synchrotron SAXS data from solutions of adenine specific DNA methyltransferase (Mod HP_0593) at pH 5.5 in 25 mM citrate, 250 mM NaCl were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
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  "guinier_point_first": 18,
  "guinier_point_last": 47,
  "pddf_point_first": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDFM6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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