6QXY

Pink beam serial crystallography: Lysozyme, 5 us exposure, 8813 patterns merged (1 chip)

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2019-03-08 Released: 2019-10-16 
  • Deposition Author(s): Lieske, J., Tolstikova, A., Meents, A.
  • Funding Organization(s): European Commission, German Federal Ministry for Education and Research, European Union, European Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report



Literature

1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector.

Tolstikova, A.Levantino, M.Yefanov, O.Hennicke, V.Fischer, P.Meyer, J.Mozzanica, A.Redford, S.Crosas, E.Opara, N.L.Barthelmess, M.Lieske, J.Oberthuer, D.Wator, E.Mohacsi, I.Wulff, M.Schmitt, B.Chapman, H.N.Meents, A.

(2019) IUCrJ 6: 927-937

  • DOI: 10.1107/S205225251900914X
  • Primary Citation of Related Structures:  
    6QXV, 6QXX, 6QXW, 6QXY, 6QY1, 6QY0, 6QY2, 6QY5, 6QY4

  • PubMed Abstract: 
  • Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we ...

    Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.


    Organizational Affiliation

    Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.86α = 90
b = 79.86β = 90
c = 38.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Commission637295
German Federal Ministry for Education and ResearchGermany031B0405D
European Union654220
European Research Council609920
German Federal Ministry for Education and ResearchGermany05K2018-201-06727 MXD

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release