6QXV

Pink beam serial crystallography: Proteinase K, 1 us exposure, 1585 patterns merged (2 chips)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.176 

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:  
    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
Proteinase KA279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.62α = 90
b = 68.62β = 90
c = 104.52γ = 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 Research Council609920
European Union654220
German Federal Ministry for Education and ResearchGermany05K2018 - 2017-06727

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references