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Showing 1 - 100 of 7,866 items (all data)


DB-ID

Resolution

Resolution Method

CTF correction

3D reconstruction Algorithm

3D reconstruction Software
PDB-6axz0.75DIFFRACTION PATTERN/LAYERLINES
EMDB-72870.85DIFFRACTION PATTERN/LAYERLINES
EMDB-88571.0DIFFRACTION PATTERN/LAYERLINES
PDB-5k2e1.0DIFFRACTION PATTERN/LAYERLINES
PDB-5k2f1.0DIFFRACTION PATTERN/LAYERLINES
PDB-5k2h1.05DIFFRACTION PATTERN/LAYERLINES
EMDB-82161.1DIFFRACTION PATTERN/LAYERLINES
PDB-5k2g1.1DIFFRACTION PATTERN/LAYERLINES
PDB-5k7n1.1DIFFRACTION PATTERN/LAYERLINES
EMDB-30011.4DIFFRACTION PATTERN/LAYERLINES
EMDB-30281.4DIFFRACTION PATTERN/LAYERLINES
EMDB-82731.4DIFFRACTION PATTERN/LAYERLINES
PDB-5ko01.4DIFFRACTION PATTERN/LAYERLINES
PDB-4znn1.41
PDB-5vos1.42DIFFRACTION PATTERN/LAYERLINES
PDB-4ril1.43
EMDB-82211.6DIFFRACTION PATTERN/LAYERLINES
PDB-5k7s1.6DIFFRACTION PATTERN/LAYERLINES
EMDB-82201.7DIFFRACTION PATTERN/LAYERLINES
PDB-5k7r1.7DIFFRACTION PATTERN/LAYERLINES
EMDB-80771.75
PDB-5i9s1.75
EMDB-81941.8FSC 0.143FREALIGN
EMDB-82171.8DIFFRACTION PATTERN/LAYERLINES
PDB-5k121.8FSC 0.143
PDB-5k7o1.8DIFFRACTION PATTERN/LAYERLINES
EMDB-29731.9DIFFRACTION PATTERN/LAYERLINES
EMDB-82721.9DIFFRACTION PATTERN/LAYERLINES
PDB-2b6o1.9
PDB-5knz1.9DIFFRACTION PATTERN/LAYERLINES
PDB-5o4w2.11DIFFRACTION PATTERN/LAYERLINES
PDB-5o4x2.11DIFFRACTION PATTERN/LAYERLINES
PDB-4d3e2.12MIX OF single particle, helical RECONSTRUCTION
EMDB-42132.14FSC 0.143RELION
EMDB-29842.2FSC 0.143, semi-independentEACH PARTICLEphase residual minimizationFREALIGN
EMDB-34572.2FSC 0.143Relion 2.0 CTF correctionRELION
EMDB-41162.2FSC 0.143RELION-based WIENER FILTERingFOURIER SPACERELION
PDB-5a1a2.2
EMDB-87622.26FSC 0.143On-the-fly CTF correction during 2D alignment and 3D reconstructionFOURIER SPACEjspr
PDB-5w3m2.26FSC 0.143
EMDB-32952.3FSC 0.143, semi-independentEACH PARTICLEscore minimizationFREALIGN
EMDB-82182.3DIFFRACTION PATTERN/LAYERLINES
PDB-5ftj2.3SCORE MINIMIZATION
PDB-5k7p2.3DIFFRACTION PATTERN/LAYERLINES
EMDB-32962.4FSC 0.143, semi-independentEACH PARTICLEscore minimizationFREALIGN
EMDB-34552.4FSC 0.143Relion 2.0 CTF correctionRELION
EMDB-34562.4FSC 0.143Relion 2.0 CTF correctionRELION
PDB-5ftk2.4SCORE MINIMIZATION
EMDB-38532.5FSC 0.143RELION
EMDB-63132.5DIFFRACTION PATTERN/LAYERLINES
EMDB-63422.5DIFFRACTION PATTERN/LAYERLINES
EMDB-70252.5FSC 0.143
EMDB-82192.5DIFFRACTION PATTERN/LAYERLINES
EMDB-82222.5DIFFRACTION PATTERN/LAYERLINES
PDB-3j6k2.5DIFFRACTION PATTERN/LAYERLINES
PDB-3m9i2.5
PDB-5k7q2.5DIFFRACTION PATTERN/LAYERLINES
PDB-5k7t2.5DIFFRACTION PATTERN/LAYERLINES
PDB-6az32.5FSC 0.143
PDB-5a3e2.501
EMDB-87542.53FSC 0.143On-the-fly CTF correction during 2D alignment and 3D reconstructionFOURIER SPACEjspr
PDB-5w3e2.53FSC 0.143
EMDB-83612.54FSC 0.143
PDB-5t5h2.54FSC 0.143
EMDB-62722.6FSC 0.143, semi-independentEACH PARTICLEprojection matchingTIGRIS, IMAGIC, FREALIGN
EMDB-82522.6FSC 0.143Amplitude correction was performed during 3D reconstructionFOURIER SPACEjspr
EMDB-87432.6FSC 0.143back projectionRELION
PDB-3j9s2.6FSC 0.143projection matching
PDB-5vy52.6FSC 0.143
EMDB-35282.7FSC 0.143back projectionRELION
EMDB-39522.7FSC 0.143RELION
EMDB-67412.7FSC 0.143
EMDB-70242.7FSC 0.143
PDB-5mm22.7FSC 0.143
PDB-5xnl2.7FSC 0.143
PDB-6az12.7FSC 0.143
EMDB-87612.71FSC 0.143On-the-fly CTF correction during 2D alignment and 3D reconstructionFOURIER SPACEjspr
PDB-5w3l2.71FSC 0.143
EMDB-81892.79FSC 0.143was performed on the fly during 2D alignment and 3D reconstructionjspr
PDB-5k0u2.79FSC 0.143
EMDB-32462.8FSC 0.143Each Imagecommon lineImagic
EMDB-62872.8FSC 0.143, gold-standardEACH PARTICLEsingle particleRelion
EMDB-64642.8FSC 0.143, semi-independentCTF parameters provided by Campbell et alTigris, Unblur, Frealign
EMDB-64702.8FSC 0.143, semi-independentby imageprojection matchingEMAN, Frealign
EMDB-65832.8FSC 0.143, gold-standardEACH PARTICLERELION
EMDB-81912.8FSC 0.143FOURIER SPACEFREALIGN
EMDB-85742.8FSC 0.143Frealign
EMDB-86042.8FSC 0.143
PDB-1at92.8DIFFRACTION PATTERN/LAYERLINES
PDB-2zz92.8
PDB-3jcs2.8FSC 0.143Maximum likelihood
PDB-5foj2.8common line
PDB-5k0z2.8FSC 0.143
PDB-5uf62.8FSC 0.143
PDB-5us72.8FSC 0.143
PDB-6bdf2.8FSC 0.143
EMDB-39512.87FSC 0.143gctf was used for CTF correctionFOURIER SPACERELION
EMDB-70832.88FSC 0.143CTF correction was performed during te map refinement in Relionback projectionRELION
PDB-6bco2.88FSC 0.143
EMDB-83142.89FSC 0.143jspr

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
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