MicroED structure of proteinase K at 1.75 A resolution

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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This is version 1.6 of the entry. See complete history


Modeling truncated pixel values of faint reflections in MicroED images.

Hattne, J.Shi, D.de la Cruz, M.J.Reyes, F.E.Gonen, T.

(2016) J Appl Crystallogr 49: 1029-1034

  • DOI: https://doi.org/10.1107/S1600576716007196
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.

  • Organizational Affiliation

    Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, VA 20147, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.317α = 90
b = 67.317β = 90
c = 101.007γ = 90
Software Package:
Software NamePurpose
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-11-23
    Changes: Other
  • Version 1.3: 2016-11-30
    Changes: Refinement description
  • Version 1.4: 2018-07-18
    Changes: Data collection, Other
  • Version 1.5: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.6: 2023-08-30
    Changes: Data collection, Database references, Refinement description