6MQV | pdb_00006mqv

Structure of HEWL from LCP injector using synchrotron radiation

• PDB DOI: https://doi.org/10.2210/pdb6MQV/pdb

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


• Deposited: 2018-10-10 Released: 2019-09-11 
• Deposition Author(s): Caradoc-Davies, T.T., Aishima, J., Berntsen, P., Hadian-Jazi, M.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

The serial millisecond crystallography instrument at the Australian Synchrotron incorporating the "Lipidico" injector.

Berntsen, P., Hadian Jazi, M., Kusel, M., Martin, A.V., Ericsson, T., Call, M.J., Trenker, R., Roque, F.G., Darmanin, C., Abbey, B.

(2019) Rev Sci Instrum 90: 085110-085110

• PubMed: 31472610 
• DOI: https://doi.org/10.1063/1.5104298
• Primary Citation Related Structures: 
  6MQV


• PubMed Abstract: 
  

  A serial millisecond crystallography (SMX) facility has recently been implemented at the macromolecular crystallography beamline, MX2 at the Australian Synchrotron. The setup utilizes a combination of an EIGER X 16M detector system and an in-house developed high-viscosity injector, "Lipidico." Lipidico uses a syringe needle to extrude the microcrystal-containing viscous media and it is compatible with commercially available syringes. The combination of sample delivery via protein crystals suspended in a viscous mixture and a millisecond frame rate detector enables high-throughput serial crystallography at the Australian Synchrotron. A hit-finding algorithm, based on the principles of "robust-statistics," is employed to rapidly process the data. Here we present the first SMX experimental results with a detector frame rate of 100 Hz (10 ms exposures) and the Lipidico injector using a mixture of lysozyme microcrystals embedded in high vacuum silicon grease. Details of the experimental setup, sample injector, and data analysis pipeline are designed and developed as part of the Australian Synchrotron SMX instrument and are reviewed here.

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Organizational Affiliation: 
• Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia.
Kusel Design, 12 Coghlan Street, Niddrie, VIC 3042, Australia.
School of Science, RMIT University, Melbourne, VIC 3000, Australia.
Department of Mathematical Sciences, Chalmers University of Technology, and The University of Gothenburg, 412 96 Göteborg, Sweden.
Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 14.35 kDa 
• Atom Count: 1,059 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.68	α = 90
b = 78.68	β = 90
c = 38.48	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Caradoc-Davies, T.T., Aishima, J., Berntsen, P., Hadian-Jazi, M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	ARC Centre of Excellence in Advanced Molecular Imaging

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary