6VHC

1.4A damaged structure of GSNQNNF used to determine initial phases from radiation damage


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.40 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Experimental Phasing of MicroED Data Using Radiation Damage.

Martynowycz, M.W.Hattne, J.Gonen, T.

(2020) Structure 28: 458

  • DOI: https://doi.org/10.1016/j.str.2020.01.008
  • Primary Citation of Related Structures:  
    6VHB, 6VHC

  • PubMed Abstract: 

    We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present an example of an experimentally phased structure using only MicroED data. The structure of a seven-residue peptide is solved starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous-rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a "low-dose dataset." The data from the second pass were similarly merged to form a "damaged dataset." Differences between these two datasets were used to identify a single heavy-atom site from a Patterson difference map, and initial phases were generated. Finally, the structure was completed by iterative cycles of modeling and refinement.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GSNQNNF7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.40 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 4.88α = 83.6
b = 14.17β = 84.98
c = 17.62γ = 83.31
Software Package:
Software NamePurpose
SHELXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description