[English] 日本語
Yorodumi
- EMDB-24080: MicroED Structure of Acetaminophen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24080
TitleMicroED Structure of Acetaminophen
Map data
Sample
  • Complex: Acetaminophen
Biological speciessynthetic construct (others)
Methodelectron crystallography
AuthorsPowell SM / Novikova IV / Evans JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)FWP 74915 United States
CitationJournal: To be Published
Title: MicroED Structure of Acetaminophen
Authors: Powell SM / Novikova IV / Evans JE
History
DepositionMay 21, 2021-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_24080.png

Downloads & links

-
Map

FileDownload / File: emd_24080.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.2 Å/pix.
x 101 pix.
= 19.723 Å		0.2 Å/pix.
x 105 pix.
= 20.504 Å		0.2 Å/pix.
x 107 pix.
= 20.895 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.19528 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-2.875063 - 12.226006
Average (Standard dev.)0.0017416013 (±1.0538799)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-20-30-21
Dimensions105107101
Spacing105107101
CellA: 20.504168 Å / B: 20.894722 Å / C: 19.723055 Å
α: 90.0 ° / β: 97.903 ° / γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Acetaminophen

EntireName: Acetaminophen
Components
  • Complex: Acetaminophen

-
Supramolecule #1: Acetaminophen

SupramoleculeName: Acetaminophen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Processingelectron crystallography
Aggregation state3D array

-
Sample preparation

BufferpH: 0.01 / Component - Name: Powder / Details: Powder

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average exposure time: 0.6 sec. / Average electron dose: 0.008 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Camera length: 751 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber intensities measured: 12102 / Number structure factors: 2348 / Fourier space coverage: 80.3 / R merge: 0.2738 / Overall phase residual: 0 / Phase error rejection criteria: 0 / High resolution: 0.65 Å

-
Atomic model buiding 1

RefinementProtocol: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more