5OSN

Crystal Structure of Bovine Enterovirus 2 determined with Serial Femtosecond X-ray Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 2.3 of the entry. See complete history

Literature

High-speed fixed-target serial virus crystallography.

Roedig, P.Ginn, H.M.Pakendorf, T.Sutton, G.Harlos, K.Walter, T.S.Meyer, J.Fischer, P.Duman, R.Vartiainen, I.Reime, B.Warmer, M.Brewster, A.S.Young, I.D.Michels-Clark, T.Sauter, N.K.Kotecha, A.Kelly, J.Rowlands, D.J.Sikorsky, M.Nelson, S.Damiani, D.S.Alonso-Mori, R.Ren, J.Fry, E.E.David, C.Stuart, D.I.Wagner, A.Meents, A.

(2017) Nat. Methods 14: 805-810

  • DOI: 10.1038/nmeth.4335
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination ...

    We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.


    Organizational Affiliation

    Diamond Light Source Limited, Didcot, UK.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Pirbright Institute, Pirbright, UK.,Institute of Photonics, University of Eastern Finland, Joensuu, Finland.,Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Paul Scherrer Institut, Villigen-PSI, Switzerland.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA.,Center for Free Electron Laser Science (CFEL), Hamburg, Germany.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A
275Enterovirus EMutation(s): 0 
Find proteins for Q65480 (Enterovirus E)
Go to UniProtKB:  Q65480
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
B
244Enterovirus EMutation(s): 0 
Find proteins for Q65480 (Enterovirus E)
Go to UniProtKB:  Q65480
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
C
243Enterovirus EMutation(s): 0 
Find proteins for Q65480 (Enterovirus E)
Go to UniProtKB:  Q65480
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
D
71Enterovirus EMutation(s): 0 
Find proteins for Q65480 (Enterovirus E)
Go to UniProtKB:  Q65480
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SPH
Query on SPH

Download SDF File 
Download CCD File 
A
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
OSF
Query on OSF

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Download CCD File 
C
octyl sulfate
C8 H17 O4 S
UZZYXUGECOQHPU-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.233 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 436.600α = 90.00
b = 436.600β = 90.00
c = 436.600γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Data collection, Database references
  • Version 2.0: 2018-10-03
    Type: Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2018-10-10
    Type: Data collection, Structure summary
  • Version 2.2: 2018-11-14
    Type: Data collection, Structure summary
  • Version 2.3: 2019-07-31
    Type: Data collection, Refinement description