scholarly journals The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography

Biochemistry ◽  
2017 ◽  
Vol 56 (36) ◽  
pp. 4751-4756 ◽  
Author(s):  
Irimpan I. Mathews ◽  
Kim Allison ◽  
Thomas Robbins ◽  
Artem Y. Lyubimov ◽  
Monarin Uervirojnangkoorn ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Room Temperature ◽  
Polyketide Synthase ◽  
Conformational Flexibility ◽  
Delivery Method ◽  
X Ray ◽  
Room Temperature Sample ◽  
Serial Crystallography ◽  
Temperature Sample

Stable sample delivery in viscous media via a capillary for serial crystallography

2020 ◽  
Vol 53 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Ki Hyun Nam
Keyword(s):  
Room Temperature ◽  
Capillary Tube ◽  
Glucose Isomerase ◽  
Low Flow ◽  
Innovative Technology ◽  
Delivery Method ◽  
Crystal Sample ◽  
X Ray ◽  
Serial Crystallography ◽  
Delivery Medium

Serial crystallography (SX) is an innovative technology in structural biology that enables the visualization of the molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample-delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques, drastically reducing sample consumption. In serial millisecond crystallography using a viscous medium via a capillary, crystals of lysozyme embedded in agarose, which produce an unstable injection stream at atmospheric pressure, and crystals of glucose isomerase embedded in gelatin, which is known to be problematic for open-extruder operation, were stably delivered at a flow rate of 100 nl min−1. The room-temperature crystal structures of lysozyme and glucose isomerase were successfully determined at 1.85 and 1.70 Å resolutions, respectively. This simple but highly efficient sample-delivery method can allow researchers to deliver crystals precisely to an X-ray beam in SX experiments.

scholarly journals Liquid sample delivery techniques for serial femtosecond crystallography

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130337 ◽  
Author(s):  
Uwe Weierstall
Keyword(s):  
Flow Rate ◽  
Free Electron ◽  
Repetition Rate ◽  
Free Electron Laser ◽  
Room Temperature ◽  
Liquid Flow Rate ◽  
Free Electron Lasers ◽  
Liquid Sample ◽  
X Ray ◽  
Serial Femtosecond Crystallography

X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques.

Determination of x-ray free electron laser power using a room-temperature calorimeter

Metrologia ◽  
2016 ◽  
Vol 53 (1) ◽  
pp. 98-102 ◽  
Author(s):  
T Tanaka ◽  
M Kato ◽  
N Saito ◽  
K Tono ◽  
M Yabashi ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Laser Power ◽  
Room Temperature ◽  
X Ray

scholarly journals Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

2015 ◽  
Vol 71 (7) ◽  
pp. 856-860 ◽  
Author(s):  
Wenting Wu ◽  
Przemyslaw Nogly ◽  
Jan Rheinberger ◽  
Leonhard M. Kick ◽  
Cornelius Gati ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Second Harmonic ◽  
Night Vision ◽  
Salt Crystallization ◽  
Time Resolved ◽  
Batch Crystallization ◽  
X Ray ◽  
Vapour Diffusion ◽  
Serial Crystallography

Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallization conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.

scholarly journals Approach of Serial Crystallography II

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 655
Author(s):  
Ki-Hyun Nam
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Cryogenic Temperature ◽  
Research Trends ◽  
Special Issue ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
Fluctuation Dynamics ◽  
Serial Crystallography

Serial crystallography (SX) is an emerging X-ray crystallographic method for determining macromolecule structures. It can address concerns regarding the limitations of data collected by conventional crystallography techniques, which require cryogenic-temperature environments and allow crystals to accumulate radiation damage. Time-resolved SX studies using the pump-probe methodology provide useful information for understanding macromolecular mechanisms and structure fluctuation dynamics. This Special Issue deals with the serial crystallography approach using an X-ray free electron laser (XFEL) and synchrotron X-ray source, and reviews recent SX research involving synchrotron use. These reports provide insights into future serial crystallography research trends and approaches.

scholarly journals Processing serial crystallography data with CrystFEL: a step-by-step guide

2019 ◽  
Vol 75 (2) ◽  
pp. 219-233 ◽  
Author(s):  
Thomas A. White
Keyword(s):  
Light Source ◽  
Free Electron ◽  
Free Electron Laser ◽  
Command Line ◽  
User Perspective ◽  
X Ray ◽  
Synchrotron Light ◽  
Serial Crystallography

This article provides a step-by-step guide to the use of the CrystFEL software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source. Whereas previous papers have described the theory and algorithms and their rationale, this paper describes the steps to be performed from a user perspective, including command-line examples.

scholarly journals The Mn 4 Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130324 ◽  
Author(s):  
Rosalie Tran ◽  
Jan Kern ◽  
Johan Hattne ◽  
Sergey Koroidov ◽  
Julia Hellmich ◽  
...  
Keyword(s):  
Free Electron ◽  
Water Oxidation ◽  
Free Electron Laser ◽  
Room Temperature ◽  
Oxidation Catalyst ◽  
Cryogenic Temperatures ◽  
New Approach ◽  
X Ray ◽  
The Past ◽  
Photosynthetic Water Oxidation

The structure of photosystem II and the catalytic intermediate states of the Mn 4 CaO 5 cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.

scholarly journals Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser

2019 ◽  
Vol 75 (7) ◽  
pp. 496-500
Author(s):  
Christopher Jones ◽  
Brandon Tran ◽  
Chelsie Conrad ◽  
Jason Stagno ◽  
Robert Trachman ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Small Molecules ◽  
Free Electron ◽  
Free Electron Laser ◽  
Room Temperature ◽  
Temperature Structure ◽  
Data Set ◽  
Time Resolved ◽  
Regulate Gene Expression ◽  
X Ray

Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5′-monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1 Å resolution. This model, which was refined against a data set from ∼750 diffraction images (each from a single crystal), was found to be consistent with that previously obtained from data collected at 100 K using conventional synchrotron X-radiation. These experiments demonstrate the feasibility of time-resolved XFEL experiments to understand how the ZTP riboswitch accommodates cognate ligand binding.

scholarly journals ClickX: a visualization-based program for preprocessing of serial crystallography data

2019 ◽  
Vol 52 (3) ◽  
pp. 674-682 ◽  
Author(s):  
Xuanxuan Li ◽  
Chufeng Li ◽  
Haiguang Liu
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Large Data ◽  
Parameter Tuning ◽  
Data File ◽  
Minimization Method ◽  
X Ray ◽  
Computing Platform ◽  
Linac Coherent Light Source ◽  
Serial Crystallography

Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.

Sign in / Sign up

Export Citation Format

Share Document