5O4X | pdb_00005o4x

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.279 (Depositor) 
  • R-Value Work: 
    0.264 (Depositor), 0.283 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5O4X

This is version 1.3 of the entry. See complete history

Literature

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

Clabbers, M.T.B.van Genderen, E.Wan, W.Wiegers, E.L.Gruene, T.Abrahams, J.P.

(2017) Acta Crystallogr D Struct Biol 73: 738-748

  • DOI: https://doi.org/10.1107/S2059798317010348
  • Primary Citation Related Structures: 
    5O4W, 5O4X

  • PubMed Abstract: 

    Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.


  • Organizational Affiliation
    • Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 28.66 kDa 
  • Atom Count: 2,000 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 258 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysozyme C
A, B
129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.11 Å
  • R-Value Free:  0.279 (Depositor) 
  • R-Value Work:  0.264 (Depositor), 0.283 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.56α = 90
b = 68.05β = 90
c = 32.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary