3J3X

Independent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (training map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM model validation using independent map reconstructions.

Dimaio, F.Zhang, J.Chiu, W.Baker, D.

(2013) Protein Sci. 22: 865-868

  • DOI: 10.1002/pro.2267

  • PubMed Abstract: 
  • An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be grea ...

    An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperonin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
532Methanococcus maripaludisMutation(s): 0 
Find proteins for Q877G8 (Methanococcus maripaludis)
Go to UniProtKB:  Q877G8
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection