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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: Jones CG / Martynowycz MW / Hattne J / Fulton TJ / Stoltz BM / Rodriguez JA / Nelson HM / Gonen T
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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

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
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
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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
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

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

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