6MH8

High-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 

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This is version 1.4 of the entry. See complete history. 


Literature

High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source.

Martin-Garcia, J.M., Zhu, L., Mendez, D., Lee, M.Y., Chun, E., Li, C., Hu, H., Subramanian, G., Kissick, D., Ogata, C., Henning, R., Ishchenko, A., Dobson, Z., Zhang, S., Weierstall, U., Spence, J.C.H., Fromme, P., Zatsepin, N.A., Fischetti, R.F., Cherezov, V., Liu, W.

(2019) IUCrJ 6: 412-425

  • DOI: 10.1107/S205225251900263X
  • Primary Citation of Related Structures:  
    6MH6, 6MH8

  • PubMed Abstract: 

    • Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources ...

    Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth ('pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A 2A adenosine receptor (A 2A AR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A 2A AR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.

    Organizational Affiliation: 

    School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine receptor A2a, Soluble cytochrome b562 chimeric constructA447Homo sapiens, Escherichia coliMutation(s): 0 
Gene Names: ADORA2A, ADORA2, cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP29274P0ABE7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZMA
Query on ZMA
Download Ideal Coordinates CCD File 
B [auth A]4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
C16 H15 N7 O2
PWTBZOIUWZOPFT-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZMA BindingDB:  6MH8 Ki: min: 0.1, max: 64 (nM) from 16 assay(s)
Kd: 0.22 (nM) from 1 assay(s)
IC50: min: 0.68, max: 81 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40α = 90
b = 179β = 90
c = 142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Precognitiondata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1231306
National Science Foundation (NSF, United States)United States1565180
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR21DA042298
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM124152
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM095583
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127086
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR24GM111072
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAGM12006
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection
  • Version 1.3: 2019-11-06
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence