6QY1

Pink beam serial crystallography: Lysozyme, 5 us exposure, 1500 patterns merged

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus

  • Deposited: 2019-03-08 Released: 2019-09-25 
  • 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: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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:  

  • 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: 

    Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,C-CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4002 Basel, Switzerland.,Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany.,Malopolska Centre of Biotechnology, Jagiellonian University, Cracow 30-387, Poland.,Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland.,Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.860α = 90.00
b = 79.860β = 90.00
c = 38.020γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Data collection, Database references