6G8B

E. coli Aminopeptidase N solved by Native SAD from a dataset collected in 60 second with JUNGFRAU detector


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector.

Leonarski, F.Redford, S.Mozzanica, A.Lopez-Cuenca, C.Panepucci, E.Nass, K.Ozerov, D.Vera, L.Olieric, V.Buntschu, D.Schneider, R.Tinti, G.Froejdh, E.Diederichs, K.Bunk, O.Schmitt, B.Wang, M.

(2018) Nat Methods 15: 799-804

  • DOI: https://doi.org/10.1038/s41592-018-0143-7
  • Primary Citation of Related Structures:  
    6G89, 6G8A, 6G8B

  • PubMed Abstract: 

    The accuracy of X-ray diffraction data is directly related to how the X-ray detector records photons. Here we describe the application of a direct-detection charge-integrating pixel-array detector (JUNGFRAU) in macromolecular crystallography (MX). JUNGFRAU features a uniform response on the subpixel level, linear behavior toward high photon rates, and low-noise performance across the whole dynamic range. We demonstrate that these features allow accurate MX data to be recorded at unprecedented speed. We also demonstrate improvements over previous-generation detectors in terms of data quality, using native single-wavelength anomalous diffraction (SAD) phasing, for thaumatin, lysozyme, and aminopeptidase N. Our results suggest that the JUNGFRAU detector will substantially improve the performance of synchrotron MX beamlines and equip them for future synchrotron light sources.


  • Organizational Affiliation

    Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminopeptidase N891Escherichia coli K-12Mutation(s): 0 
Gene Names: pepNb0932JW0915
EC: 3.4.11.2
UniProt
Find proteins for P04825 (Escherichia coli (strain K12))
Explore P04825 
Go to UniProtKB:  P04825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04825
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.109α = 90
b = 122.109β = 90
c = 172.021γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references