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Resolution Assessment in Resolution Assessment in

Resolution Assessment in - PowerPoint Presentation

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Resolution Assessment in - PPT Presentation

CryoEM Kristin Shingler Friday August 2 nd 2013 What is Resolution In short how close two objects can be without appearing as one Atomic resolution is achieved in xray crystallography ID: 557534

map resolution 2013 elife resolution map elife 2013 conventional gold standard atomic assessment reviewers sun structure nanometer nature model

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Slide1

Resolution Assessment in CryoEM

Kristin Shingler

Friday, August 2

nd

, 2013Slide2

What is Resolution?

In short, how close two objects can be without appearing as one.

Atomic resolution is achieved in x-ray crystallography.

Typically, cryoEM generates sub-nanometer resolution, but recent reconstructions have approached atomic resolution.Slide3

Semliki Forest Virus 1986

3.2 nanometer

r

esolution Vogel

et al.,

1986

NatureSlide4

Sub-nanometer Resolution

Hepatitis B Capsid, 9.1

Å

Resolution Conway

et al.,

1997

ScienceSlide5

Near-Atomic Resolution

Epsilon 15 Bacteriophage, 4.5

Å

Resolution Jiang

et al.,

2008

NatureSlide6

Atomic Resolution

Human Adenovirus 5, 3.6

Å

Resolution Liu

et al.,

2010

ScienceSlide7

What does resolution really mean?

Zhou,

Current Opinions in Structural Biology

, 2008Slide8

What does resolution really mean?

Baker

et al.

,

Methods in Enzymology

, 2010Slide9

Resolution Assessment in X-ray Crystallography

Modified Figure 5 from

Wlodawer

et al.

2007

Determined by how closely the crystal lattice can be packed, while still maintaining diffraction

Various statistical measurements correlate the resolutionSlide10

3D Reconstruction Work Flow

Baker, Olson, and Fuller 1999

Microbiology and Molecular Biology ReviewsSlide11

Fourier Shell Correlation

F

1

– Structure Factor for Map #1

F

2

– Structure Factor for Map #2

r

i

– individual voxel element

r – radius

“measures the

normliazed

cross-correlation coefficient between two 3D volumes as a function of spatial frequency” - van HeelSlide12

Conventional Resolution Estimation versus Gold Standard

Conventional

Gold Standard

Model

Even

Map

Odd

Map

FSC and Resolution Estimate

Model

Model

½

Data

Map

½

Data

Map

FSC and Resolution EstimateSlide13

Conventional Resolution Estimation versus Gold Standard

Scheres

and

Chen

e

,

2012

Nature MethodsSlide14
Slide15

Why this paper?

Elife

is an open access journal

It provides readers with both the reviewers comments AND the author’s response to reviewersAn excellent example of high quality work showing the disparity between conventional and gold standard resolution assessmentSlide16

Timeline of Events

The authors first reported the resolution of their map to be 4.6

Å by using conventional resolution assessment

This method was challenged by reviewers The authors reassessed resolution using the gold standard method and found the map was 5.3Å resolution Slide17

Reviewers Comment

Sun

et al.,

2013 ElifeSlide18

Author’s Response

Sun

et al.,

2013

ElifeSlide19

Chikungunya

Virus Structure

Sun

et al.,

2013

ElifeSlide20

CryoEM Density Fitting

Sun

et al.,

2013

Elife