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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9289 | ||||||||||||||||||
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Title | MicroED map of (+)-limaspermidine at 0.77 A resolution | ||||||||||||||||||
![]() | 2Fo-Fc map of limasperimidine | ||||||||||||||||||
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Biological species | synthetic construct (others) | ||||||||||||||||||
Method | electron crystallography / cryo EM / Resolution: 0.77 Å | ||||||||||||||||||
![]() | Jones CG / Martynowycz MW / Hattne J / Fulton T / Stoltz BM / Rodriguez JA / Nelson HM / Gonen T | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination. Authors: Christopher G Jones / Michael W Martynowycz / Johan Hattne / Tyler J Fulton / Brian M Stoltz / Jose A Rodriguez / Hosea M Nelson / Tamir Gonen / ![]() Abstract: In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful ...In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule's structure requires X-ray and/or neutron diffraction studies. In practice, however, X-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the electron cryo-microscopy (cryoEM) method microcrystal electron diffraction (MicroED) to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high-quality MicroED data from nanocrystals (∼100 nm, ∼10 g) resulting in atomic resolution (<1 Å) crystal structures in minutes. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 99.1 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.2 KB 14.2 KB | Display Display | ![]() |
Images | ![]() | 38 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 80.6 KB | Display | ![]() |
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Full document | ![]() | 79.6 KB | Display | |
Data in XML | ![]() | 495 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9282C ![]() 9283C ![]() 9284C ![]() 9285C ![]() 9286C ![]() 9287C ![]() 9288C ![]() 9290C ![]() 9291C ![]() 9292C ![]() 6mxfC C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 2Fo-Fc map of limasperimidine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.23813 Å / Y: 0.24786 Å / Z: 0.25333 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : (+)-limaspermidine
Entire | Name: (+)-limaspermidine |
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Components |
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-Supramolecule #1: (+)-limaspermidine
Supramolecule | Name: (+)-limaspermidine / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 272.217 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron crystallography |
Aggregation state | 3D array |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 / Details: Powder |
Grid | Details: unspecified |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 298 K / Details: Hand-plunged. |
Details | Powder |
Crystal formation | Details: Powder |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Digitization - Sampling interval: 28.0 µm / Number grids imaged: 1 / Number diffraction images: 124 / Average exposure time: 3.05 sec. / Average electron dose: 0.09 e/Å2 / Details: FEI CetaD |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 670 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 0.77 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystal parameters | Unit cell - A: 7.62 Å / Unit cell - B: 13.88 Å / Unit cell - C: 15.2 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 21 21 21 |
Crystallography statistics | Number intensities measured: 8252 / Number structure factors: 3430 / Fourier space coverage: 93 / R sym: 0.167 / R merge: 0.216 / Overall phase error: 63.94 / Overall phase residual: 63.94 / Phase error rejection criteria: 0 / High resolution: 0.77 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.77 Å / Shell - Low resolution: 0.79 Å / Shell - Number structure factors: 109 / Shell - Phase residual: 89.77 / Shell - Fourier space coverage: 75.17 / Shell - Multiplicity: 2.2 |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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