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- EMDB-9288: MicroED map of ibuprofen at 1.1 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-9288
TitleMicroED map of ibuprofen at 1.1 A resolution
Map data2Fo-Fc map of ibuprofen
Sample
  • Organelle or cellular component: Ibuprofen
Biological speciessynthetic construct (others)
Methodelectron crystallography / cryo EM
AuthorsJones CG / Martynowycz MW / Hattne J / Fulton T / Stoltz BM / Rodriguez JA / Nelson HM / Gonen T
Funding support United States, 5 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1650604 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080269 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128936 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128867 United States
CitationJournal: ACS Cent Sci / Year: 2018
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
DepositionOct 30, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseNov 21, 2018-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.51192
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.51192
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9288.map.gz / Format: CCP4 / Size: 36.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2Fo-Fc map of ibuprofen
Voxel sizeX: 0.36625 Å / Y: 0.32833 Å / Z: 0.33531 Å
Density
Contour LevelBy AUTHOR: 0.51192 / Movie #1: 0.51192
Minimum - Maximum-0.7866683 - 1.7580557
Average (Standard dev.)-0.0014273688 (±0.34127527)
SymmetrySpace group: 14
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions40327
Spacing402432
CellA: 14.650001 Å / B: 7.88 Å / C: 10.73 Å
α: 90.0 ° / β: 99.731 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.366250.328333333333330.3353125
M x/y/z402432
origin x/y/z0.0000.0000.000
length x/y/z14.6507.88010.730
α/β/γ90.00099.73190.000
start NX/NY/NZ000
NX/NY/NZ40732
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS32407
D min/max/mean-0.7871.758-0.001

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Supplemental data

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Sample components

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Entire : Ibuprofen

EntireName: Ibuprofen
Components
  • Organelle or cellular component: Ibuprofen

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Supramolecule #1: Ibuprofen

SupramoleculeName: Ibuprofen / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 188.138 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7 / Details: Powder
GridDetails: unspecified
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 298 K / Details: Hand-plunged.
DetailsPowder
Crystal formationDetails: Powder

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 530 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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: 129 / Average exposure time: 3.05 sec. / Average electron dose: 0.09 e/Å2 / Details: FEI CetaD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Crystal parametersUnit cell - A: 14.65 Å / Unit cell - B: 7.88 Å / Unit cell - C: 10.73 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 99.7 ° / Space group: P 21/c
Crystallography statisticsNumber intensities measured: 1452 / Number structure factors: 506 / Fourier space coverage: 54.3 / R sym: 0.147 / R merge: 0.178 / Overall phase error: 26.76 / Overall phase residual: 26.76 / Phase error rejection criteria: 0 / High resolution: 1.1 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.101 Å / Shell - Low resolution: 1.128 Å / Shell - Number structure factors: 35 / Shell - Phase residual: 37.44 / Shell - Fourier space coverage: 50.72 / Shell - Multiplicity: 3.6
Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

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