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- EMDB-7616: Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219... -

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Basic information

Entry
Database: EMDB / ID: EMD-7616
TitleRabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219k particles)
Map dataRabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219k particles)
Sample
  • Complex: Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 214k particles)
    • Protein or peptide: Rabbit muscle aldolase
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKim LK / Rice WJ / Eng ET / Kopylov M / Cheng A / Raczkowski AM / Jordan KD / Bobe D / Potter CS / Carragher B
CitationJournal: Front Mol Biosci / Year: 2018
Title: Benchmarking cryo-EM Single Particle Analysis Workflow.
Authors: Laura Y Kim / William J Rice / Edward T Eng / Mykhailo Kopylov / Anchi Cheng / Ashleigh M Raczkowski / Kelsey D Jordan / Daija Bobe / Clinton S Potter / Bridget Carragher /
Abstract: Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software ...Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis. This provides confidence that all aspects of the pipeline are capable of producing maps to high resolution. Here we describe benchmarking procedures using a test sample, rabbit muscle aldolase.
History
DepositionMar 23, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseJan 23, 2019-
UpdateJan 23, 2019-
Current statusJan 23, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.644
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.644
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7616.png

Downloads & links

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Map

FileDownload / File: emd_7616.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219k particles)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.644 / Movie #1: 0.644
Minimum - Maximum-1.9839579 - 3.9625776
Average (Standard dev.)-0.000042142347 (±0.12518694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z218.880218.880218.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.9843.963-0.000

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Supplemental data

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Half map: Rabbit muscle aldolase at 2.5 A resolution (17sep21j...

Fileemd_7616_half_map_1.map
AnnotationRabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219k particles), half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rabbit muscle aldolase at 2.5 A resolution (17sep21j...

Fileemd_7616_half_map_2.map
AnnotationRabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 219k particles), half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 214...

EntireName: Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 214k particles)
Components
  • Complex: Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 214k particles)
    • Protein or peptide: Rabbit muscle aldolase

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Supramolecule #1: Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 214...

SupramoleculeName: Rabbit muscle aldolase at 2.5 A resolution (17sep21j all img, 214k particles)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 150 KDa

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Macromolecule #1: Rabbit muscle aldolase

MacromoleculeName: Rabbit muscle aldolase / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAAWRC VLKIGEHTPS A LAIMENAN ...String:
PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAAWRC VLKIGEHTPS A LAIMENAN VLARYASICQ QNGIVPIVEP EILPDGDHDL KRCQYVTEKV LAAVYKALSD HHIYLEGTLL KPNMVTPGHA CT QKYSHEE IAMATVTALR RTVPPAVTGV TFLSGGQSEE EASINLNAIN KCPLLKPWAL TFSYGRALQA SALKAWGGKK ENL KAAQEE YVKRALANSL ACQGKYTPSG QAGAAASESL FISNHAY

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: common lines
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214000
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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