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- EMDB-9290: MicroED map of progesterone at 0.9 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-9290
TitleMicroED map of progesterone at 0.9 A resolution
Map data2Fo-Fc map of progesterone
Sample
  • Organelle or cellular component: Progesterone
Biological speciessynthetic construct (others)
Methodelectron crystallography / cryo EM / Resolution: 0.9 Å
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: 0.46494
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.46494
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9290.png

Downloads & links

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Map

FileDownload / File: emd_9290.map.gz / Format: CCP4 / Size: 88.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2Fo-Fc map of progesterone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.27 Å/pix.
x 13 pix.
= 12.81 Å		0.29 Å/pix.
x 36 pix.
= 10.38 Å		0.29 Å/pix.
x 48 pix.
= 13.89 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.28833 Å / Y: 0.26688 Å / Z: 0.28938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46494 / Movie #1: 0.46494
Minimum - Maximum-0.7666079 - 2.4950562
Average (Standard dev.)-0.00083216873 (±0.3099573)
SymmetrySpace group: 19
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions364813
Spacing364848
CellA: 10.38 Å / B: 12.809999 Å / C: 13.89 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.288333333333330.2668750.289375
M x/y/z364848
origin x/y/z0.0000.0000.000
length x/y/z10.38012.81013.890
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ361348
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS483613
D min/max/mean-0.7672.495-0.001

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Supplemental data

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Sample components

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Entire : Progesterone

EntireName: Progesterone
Components
  • Organelle or cellular component: Progesterone

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Supramolecule #1: Progesterone

SupramoleculeName: Progesterone / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 284.224 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: 90 / 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: 670 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.type: BY AUTHOR / Resolution: 0.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystal parametersUnit cell - A: 10.38 Å / Unit cell - B: 12.81 Å / Unit cell - C: 13.89 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 21 21 21
Crystallography statisticsNumber intensities measured: 4487 / Number structure factors: 1871 / Fourier space coverage: 72.1 / R sym: 0.147 / R merge: 0.18 / Overall phase error: 47.82 / Overall phase residual: 47.82 / Phase error rejection criteria: 0 / High resolution: 0.9 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.9 Å / Shell - Low resolution: 0.923 Å / Shell - Number structure factors: 77 / Shell - Phase residual: 65.92 / Shell - Fourier space coverage: 71.92 / Shell - Multiplicity: 2.4

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

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