6FJS

Proteinase~K SIRAS phased structure of room-temperature, serially collected synchrotron data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

De novoprotein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography.

Botha, S.Baitan, D.Jungnickel, K.E.J.Oberthur, D.Schmidt, C.Stern, S.Wiedorn, M.O.Perbandt, M.Chapman, H.N.Betzel, C.

(2018) IUCrJ 5: 524-530

  • DOI: 10.1107/S2052252518009223

  • PubMed Abstract: 
  • During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the applicat ...

    During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.


    Organizational Affiliation

    Xtal Concepts GmbH, Marlowring 19, 22525 Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.,Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.,Institute of Biochemistry and Molecular Biology, Chemistry Department, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany.




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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.142 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.550α = 90.00
b = 67.550β = 90.00
c = 107.400γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PDB_EXTRACTdata extraction
SHELXDEphasing
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release