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- EMDB-7617: Rabbit muscle aldolase at 2.5 A resolution (17sep21j less 25nm ic... -

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Basic information

Entry
Database: EMDB / ID: EMD-7617
TitleRabbit muscle aldolase at 2.5 A resolution (17sep21j less 25nm ice thickness, 124k particles)
Map data
SampleRabbit muscle aldolase at 2.5 A resolution (17sep21j <25nm ice thickness, 124K particles):
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: 0.589
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.589
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7617.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.589 / Movie #1: 0.589
Minimum - Maximum-1.662178 - 3.344108
Average (Standard dev.)-0.0016381869 (±0.108426906)
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-1.6623.344-0.002

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Supplemental data

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Half map: Rabbit muscle aldolase at 2.5 A resolution (17sep31j...

Fileemd_7617_half_map_1.map
AnnotationRabbit muscle aldolase at 2.5 A resolution (17sep31j <25nm ice thickness, 124K particles), half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Rabbit muscle aldolase at 2.5 A resolution (17sep31j...

Fileemd_7617_half_map_2.map
AnnotationRabbit muscle aldolase at 2.5 A resolution (17sep31j <25nm ice thickness, 124K particles), half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Rabbit muscle aldolase at 2.5 A resolution (17sep21j <25nm ice th...

EntireName: Rabbit muscle aldolase at 2.5 A resolution (17sep21j <25nm ice thickness, 124K particles) / Number of Components: 2

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Component #1: protein, Rabbit muscle aldolase at 2.5 A resolution (17sep21j <25...

ProteinName: Rabbit muscle aldolase at 2.5 A resolution (17sep21j <25nm ice thickness, 124K particles) / Recombinant expression: No
MassExperimental: 150 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Rabbit muscle aldolase

ProteinName: Rabbit muscle aldolase / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 65 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: D2 (2x2 fold dihedral) / Number of Projections: 124000
3D reconstructionResolution: 2.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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