| Literature DB >> 32876583 |
Anastasya Shilova1, Hugo Lebrette2, Oskar Aurelius1, Jie Nan1, Martin Welin3, Rebeka Kovacic3, Swagatha Ghosh4, Cecilia Safari4, Ross J Friel5, Mirko Milas1, Zdenek Matej1, Martin Högbom2, Gisela Brändén4, Marco Kloos6, Robert L Shoeman7, Bruce Doak7, Thomas Ursby1, Maria Håkansson3, Derek T Logan3, Uwe Mueller1.
Abstract
Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed. open access.Entities:
Keywords: high-viscosity injectors; macromolecular crystallography; sample delivery; serial crystallography
Mesh:
Substances:
Year: 2020 PMID: 32876583 PMCID: PMC7467353 DOI: 10.1107/S1600577520008735
Source DB: PubMed Journal: J Synchrotron Radiat ISSN: 0909-0495 Impact factor: 2.616
Figure 1Schematic representation of MAX IV Laboratory photon sources and beamlines (credit: Johnny Kvistholm, MAX IV Laboratory).
Figure 2(a) SSX raster scan set up at BioMAX. A silicon nitride membrane is mounted on the goniometer head [see panel (d]. (b) Setup for SSX using XtalTool and a humidifier. (c) Crystals grown on a 24-well VDX-plate using XtalTool. (d) Omega goniometer head with mounted silicon nitride membrane sandwich. (e) 10 µm-sized crystals distributed on silicon nitride membranes.
Figure 3(a) HVE injector mounted and prepared for the experiment. The water line is connected to the HPLC pump and is regulated to control the sample extrusion rate. The gas line is connected to a pressurized helium gas cylinder which is controlled for a stable extrusion path. The blue fitting can be optionally connected to the thermostat to maintain a stable sample temperature inside the reservoir. (b) Schematic representation of the HVE injector (adapted from the original design by Bruce Doak). The sample shown in green is pushed by a plunger with a PTFE ball at the end through the silica capillary. (c) Schematic representation of the end of the injector nozzle. The sample travels through the silica capillary (yellow) and is exposed to the X-rays at the exit. The gas stream travels through the injector down to the borosilicate capillary to stabilize the extrusion.
Data collection and refinement statistics for the proteins used
Values in parentheses are for the highest resolution shell.
| Galectin-3C with lactose | R2 | CcO in LCP | ||
|---|---|---|---|---|
| Sample delivery method | Fixed target (XtalTool with humidifier) | Fixed target (silicon nitride membranes) | Fixed target (silicon nitride membranes) | HVE-injector |
| Total amount of used sample (µl) | 4 | 0.8 | 0.8 | 100 |
| Flux dimension (photons s−1) | 2 × 1012 | 2 × 1012 | 2 × 1012 | |
| Beam size (µm × µm) | 20 × 5 | 20 × 5 | 20 × 5 | |
| Data collection temperature (K) | 298 | 298 | 298 | |
| Exposure time per image (s) | 0.05 | 0.05 | 0.01 | |
| Estimated dose per crystal (MGy) | 0.68 | 0.68 | 0.25 | |
| No. of collected images | 70537 | 32303 | 68061 | 214170 |
| Average hit rate (%) | 70.1 | 65.1 | 58.1 | 4.7 |
| Indexing rate (%) | 31.5 | 27.3 | 56.2 | 64.7 |
| No. of indexed images | 15555 | 13522 | 22224 | 6513 |
| No. of total / unique reflections | 2161463 / 15552 | 2762267 / 14154 | 12701350 / 24094 | 459543 / 23306 |
| Multiplicity | 139 | 195 | 527 | 20 |
| Space group |
|
|
| |
| Cell dimensions | 36.6, 58.1, 63.7 | 35.7, 56.4, 61.7 | 64.3, 64.3, 153.2 | 145.2, 100.2, 96.6 |
| α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90.0, 126.6, 90.0 | |
| Completeness (%) | 99.9 | 96.3 | 98.6 | 99.7 |
|
| 5.66 (2.5) | 5.32 (2.1) | 6.73 (2.2) | 2.93 (2.0) |
| Resolution range (Å) | 60–1.70 (1.75–1.70) | 61–1.70 (1.83–1.70) | 59.3–2.4 (2.58–2.4) | 77.5–3.6 (3.66–3.6) |
|
| 14.1 (37) | 15.5 (50) | 8.60 (64) | 31.5 (53) |
|
| 0.96 (0.86) | 0.96 (0.63) | 0.99 (0.64) | 0.90 (0.59) |
|
| 17.2 / 20.1 (30.9 / 42.0) | 17.0 / 19.2 (26.9 / 29.7) | 17.3 / 22.1 (23.0 / 25.9) | 31.2 / 32.5 (33.4 / 38.6) |
| No. of atoms | 1248 | 1244 | 2542 | 5951 |
| Protein | 1108 | 1149 | 2517 | 751 |
| Water | 116 | 72 | 23 | N/A |
| Ligands | 24 | 23 | 2 | N/A |
| R.m.s.d. for bonds (Å) | 0.010 | 0.020 | 0.003 | 0.003 |
| R.m.s.d. for angles (°) | 1.2 | 1.5 | 0.49 | 0.76 |
| Average | 21 | 26 | 90 | 88 |
| Ramachandran plot statistics | ||||
| Favoured (%) | 97.8 | 97.7 | N/A | |
| Allowed (%) | 2.2 | 2.32 | N/A | |
| Disallowed (%) | 0 | 0 | N/A | |
| Rotamer outliers | 0 | 0 | N/A | |
| PDB entry | 6y4c | 6y78 | 6y2n | N/A |
Figure 4Left: microcrystals of galectin. Right: 2mF o − DF c simulated annealing omit map, omitting only the lactose residue contoured at 1σ.
Figure 5(a) R2 protein microcrystals. (b) Overall structure of the R2 protein. (c) 2m|F o| − D|F c| electron density map contoured at 1σ near one of the α-helices in the R2 structure.