5HL4

Acoustic injectors for drop-on-demand serial femtosecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb5HL4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Sinorhizobium meliloti 1021
• Mutation(s): No 


• Deposited: 2016-01-14 Released: 2016-01-27 
• Deposition Author(s): Roessler, C.G., Agarwal, R., Allaire, M., Alonso-Mori, R., Andi, B., Bachega, J.F.R., Bommer, M., Brewster, A.S., Browne, M.C., Chatterjee, R., Cho, E., Cohen, A.E., Cowan, M., Datwani, S., Davidson, V.L., Defever, J., Eaton, B., Ellson, R., Feng, Y., Ghislain, L.P., Glownia, J.M., Han, G., Hattne, J., Hellmich, J., Heroux, A., Ibrahim, M., Kern, J., Kuczewski, A., Lemke, H.T., Liu, P., Majlof, L., McClintock, W.M., Myers, S., Nelsen, S., Olechno, J., Orville, A.M., Sauter, N.K., Soares, A.S., Soltis, M.S., Song, H., Stearns, R.G., Tran, R., Tsai, Y., Uervirojnangkoorn, M., Wilmot, C.M., Yachandra, V., Yano, J., Yukl, E.T., Zhu, D., Zouni, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.330 
• R-Value Work: 0.269 
• R-Value Observed: 0.272 

Literature

Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography.

Roessler, C.G., Agarwal, R., Allaire, M., Alonso-Mori, R., Andi, B., Bachega, J.F., Bommer, M., Brewster, A.S., Browne, M.C., Chatterjee, R., Cho, E., Cohen, A.E., Cowan, M., Datwani, S., Davidson, V.L., Defever, J., Eaton, B., Ellson, R., Feng, Y., Ghislain, L.P., Glownia, J.M., Han, G., Hattne, J., Hellmich, J., Heroux, A., Ibrahim, M., Kern, J., Kuczewski, A., Lemke, H.T., Liu, P., Majlof, L., McClintock, W.M., Myers, S., Nelsen, S., Olechno, J., Orville, A.M., Sauter, N.K., Soares, A.S., Soltis, S.M., Song, H., Stearns, R.G., Tran, R., Tsai, Y., Uervirojnangkoorn, M., Wilmot, C.M., Yachandra, V., Yano, J., Yukl, E.T., Zhu, D., Zouni, A.

(2016) Structure 24: 631-640

• PubMed: 26996959 
• DOI: https://doi.org/10.1016/j.str.2016.02.007
• Primary Citation of Related Structures:  
  5F81, 5HL4, 5HQD


• PubMed Abstract: 
  

  X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.

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Organizational Affiliation: 

Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 46.82 kDa 
• Atom Count: 3,305 
• Modelled Residue Count: 397 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ring-hydroxylating dioxygenase	A	412	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMa0751
UniProt
Find proteins for Q92ZP9 (Rhizobium meliloti (strain 1021)) Explore Q92ZP9  Go to UniProtKB:  Q92ZP9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
NCO	D [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.330 
• R-Value Work: 0.269 
• R-Value Observed: 0.272 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.427	α = 90
b = 98.427	β = 90
c = 180.087	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
cctbx.xfel	data reduction
cctbx.xfel	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Roessler, C.G., Agarwal, R., Allaire, M., Alonso-Mori, R., Andi, B., Bachega, J.F.R., Bommer, M., Brewster, A.S., Browne, M.C., Chatterjee, R., Cho, E., Cohen, A.E., Cowan, M., Datwani, S., Davidson, V.L., Defever, J., Eaton, B., Ellson, R., Feng, Y., Ghislain, L.P., Glownia, J.M., Han, G., Hattne, J., Hellmich, J., Heroux, A., Ibrahim, M., Kern, J., Kuczewski, A., Lemke, H.T., Liu, P., Majlof, L., McClintock, W.M., Myers, S., Nelsen, S., Olechno, J., Orville, A.M., Sauter, N.K., Soares, A.S., Soltis, M.S., Song, H., Stearns, R.G., Tran, R., Tsai, Y., Uervirojnangkoorn, M., Wilmot, C.M., Yachandra, V., Yano, J., Yukl, E.T., Zhu, D., Zouni, A.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2016-04-06
  Changes: Database references
• Version 1.2: 2016-04-20
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Data collection
• Version 1.4: 2018-11-14
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Refinement description