[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleBenchmarking cryo-EM Single Particle Analysis Workflow.
Journal, issue, pagesFront Mol Biosci, Vol. 5, Page 50, Year 2018
Publish dateJun 4, 2018
AuthorsLaura Y Kim / William J Rice / Edward T Eng / Mykhailo Kopylov / Anchi Cheng / Ashleigh M Raczkowski / Kelsey D Jordan / Daija Bobe / Clinton S Potter / Bridget Carragher /
PubMed AbstractCryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software ...Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis. This provides confidence that all aspects of the pipeline are capable of producing maps to high resolution. Here we describe benchmarking procedures using a test sample, rabbit muscle aldolase.
External linksFront Mol Biosci / PubMed:29951483 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 4.6 Å
Structure data

EMDB-7528:
Rabbit muscle aldolase at 2.8 A (17dec27a- 1st 382 img)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-7541:
Rabbit muscle aldolase at 2.4A resolution (17dec27a 205k particles, all images)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-7550:
Rabbit muscle aldolase at 2.4A resolution (17dec27a 205k particles, all images)
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-7551:
Rabbit muscle aldolase at 3.0A resolution (17nov02c all img, 204k particles)
Method: EM (single particle) / Resolution: 3 Å

EMDB-7562:
Rabbit muscle aldolase at 3.5 A resolution (17nov02c less 25nm ice thickness, 22k particles)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-7614:
Rabbit muscle aldolase at 2.8 A resolution (17sep21j 1st 500 img, 62k particles)
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-7615:
Rabbit muscle aldolase at 4.6 A resolution (17nov02c 1st700 img, 75k particles)
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-7616:
Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219k particles)
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-7617:
Rabbit muscle aldolase at 2.5 A resolution (17sep21j less 25nm ice thickness, 124k particles)
Method: EM (single particle) / Resolution: 2.5 Å

Source
  • Oryctolagus cuniculus (rabbit)

+
About Yorodumi Papers

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more