Proteopedia - User contributions [en]

Resolution

2009-11-18T11:52:34Z

YongLiang Jiang:

<table align="right" border="0"><tr><td>
[[Image:Resolution-holton-5.0.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-3.5.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-2.5.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-1.4.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-0.5.png]]
</td></tr></table>

Resolution is an average value for the uncertainty of atomic positions in a crystallographic model, but not the minimum distance we can distinguish. High values for resolution (e.g. 5.0 Å) mean high uncertainty, and low values (e.g. 1.0 Å) mean much less uncertainty. '''2.05 Å''' is the '''median''' resolution for X-ray crystallographic results in the Protein Data Bank (43,066 on May 2, 2008).

The uncertainty for each atom is quantitated in its [[Temperature_value|temperature value]].

The '''images at right''' show how the electron density map<ref name="edm">Electron density maps are the results of [[X-ray crystallography]] experiments.</ref><ref name="stills">These are "perfect" electron density maps calculated from the atomic model (R factor = 0.0%, perfect phases and amplitudes, contoured at 1 sigma). Electron density maps based on experimental data would fit the true conformation less well. Because these electron density maps were calculated from an atomic model that lacked hydrogen atoms, the electron densities for hydrogen atoms that would appear with experimental data at a resolution of 0.5 Å do not appear.</ref> becomes more accurate and detailed as the uncertainty (resolution value) decreases from 5.0 Å to 0.5 Å.

The images at right were taken from a movie<ref>The movie ([[Image:Resolution_holton.mpeg]]) was created by James Holton at the Advanced Light Source of the Berkeley Laboratory at the University of California. Holton kindly gave explicit permission to use this movie in Proteopedia. The original source was http://ucxray.berkeley.edu/~jamesh/movies.</ref> in which the atomic model and electron density map rock back and forth while the resolution value (uncertainty) increases from 0.5 to 5.0 Å.
<center><big>
[http://proteopedia.org/wiki/images/1/1a/Resolution_holton.mpeg '''PLAY MOVIE''']
</big></center>
At 0.5 Å in the movie, every atom<ref name="stills" /> of the tryptophan sidechain in the top center of the frame is clearly represented by a sphere of electron density. At 2.5 Å (a bit worse than the median in the [[PDB]]), the overall shape and position of the Trp sidechain is still clear, as is the alpha helical conformation of the main chain. However, at 5.0 Å, only an ill-fitting bump is present to signal the bulky Trp sidechain, and the alpha helix becomes a cylinder of electron density, from which the handedness of the helix may not be discernable.

==See Also==

*[[R value]]
*[[Free R]]
*[[Believe It or Not]]

==Websites==

*[http://proteinexplorer.org/igloss.htm#resolution Resolution] at ProteinExplorer.Org's Glossary.

*[http://www.umass.edu/molvis/workshop/imgs/res-edm.htm Resolution vs. Electron Density Maps].

*[http://www.usm.maine.edu/~rhodes/ModQual/ A Glossary of Terms from Crystallography, NMR, and Homology Modeling]

==Notes==
<references/>

Resolution

2009-11-18T07:29:52Z

YongLiang Jiang:

<table align="right" border="0"><tr><td>
[[Image:Resolution-holton-5.0.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-3.5.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-2.5.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-1.4.png]]
</td></tr><tr><td>
[[Image:Resolution-holton-0.5.png]]
</td></tr></table>

Resolution is an average value for the uncertainty of atomic positions in a crystallographic model but not the minimun diatance we can distinguish. High values for resolution (e.g. 5.0 Å) mean high uncertainty, and low values (e.g. 1.0 Å) mean much less uncertainty. '''2.05 Å''' is the '''median''' resolution for X-ray crystallographic results in the Protein Data Bank (43,066 on May 2, 2008).

The uncertainty for each atom is quantitated in its [[Temperature_value|temperature value]].

The '''images at right''' show how the electron density map<ref name="edm">Electron density maps are the results of [[X-ray crystallography]] experiments.</ref><ref name="stills">These are "perfect" electron density maps calculated from the atomic model (R factor = 0.0%, perfect phases and amplitudes, contoured at 1 sigma). Electron density maps based on experimental data would fit the true conformation less well. Because these electron density maps were calculated from an atomic model that lacked hydrogen atoms, the electron densities for hydrogen atoms that would appear with experimental data at a resolution of 0.5 Å do not appear.</ref> becomes more accurate and detailed as the uncertainty (resolution value) decreases from 5.0 Å to 0.5 Å.

The images at right were taken from a movie<ref>The movie ([[Image:Resolution_holton.mpeg]]) was created by James Holton at the Advanced Light Source of the Berkeley Laboratory at the University of California. Holton kindly gave explicit permission to use this movie in Proteopedia. The original source was http://ucxray.berkeley.edu/~jamesh/movies.</ref> in which the atomic model and electron density map rock back and forth while the resolution value (uncertainty) increases from 0.5 to 5.0 Å.
<center><big>
[http://proteopedia.org/wiki/images/1/1a/Resolution_holton.mpeg '''PLAY MOVIE''']
</big></center>
At 0.5 Å in the movie, every atom<ref name="stills" /> of the tryptophan sidechain in the top center of the frame is clearly represented by a sphere of electron density. At 2.5 Å (a bit worse than the median in the [[PDB]]), the overall shape and position of the Trp sidechain is still clear, as is the alpha helical conformation of the main chain. However, at 5.0 Å, only an ill-fitting bump is present to signal the bulky Trp sidechain, and the alpha helix becomes a cylinder of electron density, from which the handedness of the helix may not be discernable.

==See Also==

*[[R value]]
*[[Free R]]
*[[Believe It or Not]]

==Websites==

*[http://proteinexplorer.org/igloss.htm#resolution Resolution] at ProteinExplorer.Org's Glossary.

*[http://www.umass.edu/molvis/workshop/imgs/res-edm.htm Resolution vs. Electron Density Maps].

*[http://www.usm.maine.edu/~rhodes/ModQual/ A Glossary of Terms from Crystallography, NMR, and Homology Modeling]

==Notes==
<references/>

Spr0440

2009-11-14T02:46:16Z

YongLiang Jiang:

Image:Example.jpg]]<applet load='3gdb' size='300' frame='true' align='right' caption='Insert caption here' />

{{STRUCTURE_3gdb | PDB=3gdb | SCENE=3gdb }}

Crystal structure of '''Spr0440''' glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

Introduction：
Endo-beta-D-glucosaminidases from family 85 of glycoside hydrolases(GH85 endohexosaminidases) act to
cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans.

Spr0440

2009-11-14T02:42:32Z

YongLiang Jiang:

Image:Example.jpg]]<applet load='3gdb' size='300' frame='true' align='right' caption='Insert caption here' />

{{STRUCTURE_3gdb | PDB=3gdb | SCENE=3gdb }}

Crystal structure of '''Spr0440''' glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6
Introduction
Endo-beta-D-glucosaminidases from family 85 of glycoside hydrolases(GH85 endohexosaminidases) act to
cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans.

Spr0440

2009-11-14T02:23:34Z

YongLiang Jiang:

[[Image:Example.jpg]]<applet load='3gdb' size='300' frame='true' align='right' caption='Insert caption here' />

{{STRUCTURE_3gdb | PDB=3gdb | SCENE=3gdb }}

Crystal structure of '''Spr0440''' glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

Spr0440

2009-10-27T01:06:07Z

YongLiang Jiang: /* This is a placeholder */

<applet load='3gdb' size='300' frame='true' align='right' caption='Insert caption here' />

{{STRUCTURE_3gdb | PDB=3gdb | SCENE=3gdb }}

Crystal structure of '''Spr0440''' glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6

Spr0440

2009-10-27T01:04:03Z

YongLiang Jiang: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...

==This is a placeholder==
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placing a Jmol applet on your page. At any time, click
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Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3gdb | PDB=3gdb | SCENE=3gdb }}

Crystal structure of '''Spr0440''' glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6