2JIC

High resolution structure of xylanase-II from one micron beam experiment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Protein Crystallography with a Micrometre-Sized Synchrotron-Radiation Beam.

Moukhametzianov, R.Burghammer, M.Edwards, P.C.Petitdemange, S.Popov, D.Fransen, M.Mcmullan, G.Schertler, G.F.Riekel, C.

(2008) Acta Crystallogr D Biol Crystallogr 64: 158

  • DOI: https://doi.org/10.1107/S090744490705812X
  • Primary Citation of Related Structures:  
    2JIC

  • PubMed Abstract: 

    For the first time, protein microcrystallography has been performed with a focused synchrotron-radiation beam of 1 microm using a goniometer with a sub-micrometre sphere of confusion. The crystal structure of xylanase II has been determined with a flux density of about 3 x 10(10) photons s(-1) microm(-2) at the sample. Two sets of diffraction images collected from different sized crystals were shown to comprise data of good quality, which allowed a 1.5 A resolution xylanase II structure to be obtained. The main conclusion of this experiment is that a high-resolution diffraction pattern can be obtained from 20 microm(3) crystal volume, corresponding to about 2 x 10(8) unit cells. Despite the high irradiation dose in this case, it was possible to obtain an excellent high-resolution map and it could be concluded from the individual atomic B-factor patterns that there was no evidence of significant radiation damage. The photoelectron escape from a narrow diffraction channel is a possible reason for reduced radiation damage as indicated by Monte Carlo simulations. These results open many new opportunities in scanning protein microcrystallography and make random data collection from microcrystals a real possibility, therefore enabling structures to be solved from much smaller crystals than previously anticipated as long as the crystallites are well ordered.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XYLANASE-II190Trichoderma longibrachiatumMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for F8W669 (Trichoderma longibrachiatum)
Explore F8W669 
Go to UniProtKB:  F8W669
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W669
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.57α = 90
b = 38.83β = 110.61
c = 57.34γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description