4N4Z

Trypanosoma brucei procathepsin B structure solved by Serial Microcrystallography using synchrotron radiation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Serial crystallography on in vivo grown microcrystals using synchrotron radiation.

Gati, C.Bourenkov, G.Klinge, M.Rehders, D.Stellato, F.Oberthur, D.Yefanov, O.Sommer, B.P.Mogk, S.Duszenko, M.Betzel, C.Schneider, T.R.Chapman, H.N.Redecke, L.

(2014) IUCrJ 1: 87-94

  • DOI: 10.1107/S2052252513033939

  • PubMed Abstract: 
  • Crystal structure determinations of biological macromolecules are limited by the availability of sufficiently sized crystals and by the fact that crystal quality deteriorates during data collection owing to radiation damage. Exploiting a micrometre-s ...

    Crystal structure determinations of biological macromolecules are limited by the availability of sufficiently sized crystals and by the fact that crystal quality deteriorates during data collection owing to radiation damage. Exploiting a micrometre-sized X-ray beam, high-precision diffractometry and shutterless data acquisition with a pixel-array detector, a strategy for collecting data from many micrometre-sized crystals presented to an X-ray beam in a vitrified suspension is demonstrated. By combining diffraction data from 80 Trypanosoma brucei procathepsin B crystals with an average volume of 9 µm(3), a complete data set to 3.0 Å resolution has been assembled. The data allowed the refinement of a structural model that is consistent with that previously obtained using free-electron laser radiation, providing mutual validation. Further improvements of the serial synchrotron crystallography technique and its combination with serial femtosecond crystallography are discussed that may allow the determination of high-resolution structures of micrometre-sized crystals.


    Organizational Affiliation

    Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY) , Notkestrasse 85, 22607 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine peptidase C (CPC)
A
340Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
EC: 3.4.22.-
Find proteins for D6XHE1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  D6XHE1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.420α = 90.00
b = 124.420β = 90.00
c = 53.770γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Data collection, Refinement description