5I9S

MicroED structure of proteinase K at 1.75 A resolution


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.75 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

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: 10.1107/S1600576716007196

  • 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, particula ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteinase K
A
279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Parengyodontium album)
Go to UniProtKB:  P06873
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.75 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 
  • Diffraction Data DOI: 
    10.15785/SBGRID/262 SBGrid
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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