5FGX

Thaumatin solved by native sulphur SAD using synchrotron radiation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.134 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data.

Nass, K.Meinhart, A.Barends, T.R.Foucar, L.Gorel, A.Aquila, A.Botha, S.Doak, R.B.Koglin, J.Liang, M.Shoeman, R.L.Williams, G.Boutet, S.Schlichting, I.

(2016) Iucrj 3: 180-191

  • DOI: 10.1107/S2052252516002980
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complica ...

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thaumatin-1
A
207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Go to UniProtKB:  P02883
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.134 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.129 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.740α = 90.00
b = 57.740β = 90.00
c = 149.980γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
XSCALEdata scaling
XDSdata reduction
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