Resolution: Difference between revisions
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<table align="right" border="0"><tr><td> | <table align="right" border="0" width="200"><tr><td> | ||
[[Image:Resolution-holton-5.0.png]] | [[Image:Resolution-holton-5.0.png]] | ||
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[[Image:Resolution-holton-0.5.png]] | [[Image:Resolution-holton-0.5.png]] | ||
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Snapshots from the movie (see below) by James Holton. See ''Limitations of the Movie'' below. | |||
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''Resolution'', in structure determinations, is the distance corresponding to the smallest observable feature: if two objects are closer than this distance, they appear as one combined blob rather than two separate objects. | |||
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[[Image:Leu425-ala426-temp12-17(av15)-1io1-labeled-300px.png|250px]] | |||
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Details at <ref>[[Introduction_to_molecular_visualization#Slabbing|Slabbed]] image from [http://www.bioinformatics.org/molvis/edm/ Electron Density] at 1.0 σ showing Leu425 and Ala426 in [[1io1]]. Temperature factors in those two residues range from 12 to 17, average 15. Separate red atom at right is a water oxygen.</ref>. | |||
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<font color="#509050">Electron<br>Density<br>Map</font> | |||
([[Electron density map|?]]) | |||
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[[Image:Leu5-ala4-temp3-12(av5)-3hyd-labeled.png]] | |||
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Details at <ref>[[Introduction_to_molecular_visualization#Slabbing|Slabbed]] image from [http://www.bioinformatics.org/molvis/edm/edm2.htm Electron Density Map] at 1.0 σ showing Leu5 and Ala4 in [[3hyd]]. [[Temperature factors]] in those two residues range from 3 to 12, average 5.</ref>. | |||
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[[Image:4gcf-ile98-val99-temp32-40(35).png]] | |||
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Details at <ref>[[Introduction_to_molecular_visualization#Slabbing|Slabbed]] image showing [[electron density map]] at 1.0 &sigma: Ile98 and Val99 in [[4gcf]]. [[Temperature factors]] in those two residues range from 32 to 45, average 37.</ref>. | |||
</td></tr></table> | </td></tr></table> | ||
Structure determination by [[X-ray crystallography]] or [[cryo-electron microscopy]] produces an [[electron density map]] (shown in <font color="#508050"><b>green</b></font>). The atomic model, shown as sticks, is then built, guided by the electron density map. | |||
'''2.05 Å''' is the '''median''' resolution for [[X-ray crystallography|X-ray crystallographic]] results in the Protein Data Bank ( | In X-ray crystallography, resolution is the smallest distance between crystal lattice planes that is resolved in the diffraction pattern. High numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution. | ||
'''2.05 Å''' is the '''median''' resolution for [[X-ray crystallography|X-ray crystallographic]] results in the Protein Data Bank (135,762 on May 19, 2019). For comparison, the van der Waals diameter of a carbon atom is 3.4-3.7 Å<ref name="atomsize">See [http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page) Atomic radii of the elements (Wikipedia)], and [http://chemwiki.ucdavis.edu/Theoretical_Chemistry/Chemical_Bonding/General_Principles/Covalent_Bond_Distance,_Radius_and_van_der_Waals_Radius values from an Inorganic Chemistry textbook].</ref>, and the length of a covalent carbon-carbon bond is 1.5 Å<ref name="atomsize" />. | |||
If some portions of the macromolecule are less ordered in the crystal than others, these will have a poorer resolution. The "resolution of the crystal" represents the most ordered portions (see [[#Determination of Resolution|Determination of Resolution]]). | If some portions of the macromolecule are less ordered in the crystal than others, these will have a poorer resolution. The "resolution of the crystal" represents the most ordered portions (see [[#Determination of Resolution|Determination of Resolution]]). | ||
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==Quick Guide== | ==Quick Guide== | ||
Here is a quick guide for interpreting values of resolution. | Here is a quick guide for interpreting values of resolution (taken from [[FirstGlance in Jmol]]). | ||
*1.2 | *< ~1.7 Å: Most atoms very clearly seen. | ||
*2. | *~1.7 - 2.2 Å: Many atoms clearly seen. | ||
*3.5 | *~2.2 - 2.8 Å: Shapes of larger sidechains seen. | ||
*5.0 | *~2.8 - 3.5 Å: Secondary structure & bulky groups seen. Atoms unclear. | ||
*~3.5 - 4.0 Å: Most [[chains]] traceable. Atoms unclear. | |||
*~4.0 - 6.0 Å: Some chains traceable. Atoms unclear. | |||
*~6.0 - 8.0 Å: Shapes of [[domains]] at best. Atoms unclear. | |||
*> ~8.0 Å: Largest features seen roughly. Atoms unclear. | |||
Bear in mind that the resolution value represents the "best" (most ordered) parts of a crystal, and that other parts may have poorer quality. The [[temperature value]] for each atom in a crystallographic model indicates the clarity of its electron density map. | |||
==Confusion of high vs. low resolution== | ==Confusion of high vs. low resolution== | ||
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==Electron Density Map vs. Resolution== | ==Electron Density Map vs. Resolution== | ||
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 resolution value decreases from 5.0 Å to 0.5 Å. | The '''images at right (top of this page)''' 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 [[Hydrogen in macromolecular models|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 resolution value decreases from 5.0 Å to 0.5 Å. | ||
The images at right were taken from a movie<ref name='movie'>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. | The images at right were taken from a movie<ref name='movie'>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. | ||
< | <br> | ||
<html5media height="315" width="560">http://www.youtube.com/embed/omFOLG5Z5w4</html5media> | |||
< | <br>Movie by James Holton at the Advanced Light Source of the Berkeley Laboratory at the University of California<ref name='movie' />.) | ||
<br>This movie is not entirely realistic. '''Limitations''' are described in the footnote<ref name="stills" />. | |||
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<!--COMMENTED OUT BY ERIC MARTZ MAY 15, 2014: I'M NOT SURE WHAT THIS TABLE WAS SUPPOSED TO ACCOMPLISH BUT IT BROKE THE LINK TO THE MOVIE! | <!--COMMENTED OUT BY ERIC MARTZ MAY 15, 2014: I'M NOT SURE WHAT THIS TABLE WAS SUPPOSED TO ACCOMPLISH BUT IT BROKE THE LINK TO THE MOVIE! | ||
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Once refinement of the electron density map is completed, the amount of electron density at the position of each atom determines that atom's [[Temperature|B factor or temperature value]]. | Once refinement of the electron density map is completed, the amount of electron density at the position of each atom determines that atom's [[Temperature|B factor or temperature value]]. | ||
==Resolution and structure quality== | |||
The higher the resolution of the diffraction data, the more measurements are present to base the model on. Also, an increase in resolution means that a given reflection is measured with less error than in a corresponding lower quality diffraction data set. As a consequence, the model can be built with fewer systematic errors (such as missing or misplaced atoms) and with less average coordinate error. The coordinate error (roughly defined as how different two models would be based on the same crystals, but independent measurement, model building and refinement) correlates with resolution, but is of a different order of magnitude. It is also influenced by completeness of the data (higher is better), the free R-factor of the refinement (lower is better), and the completeness of the model (higher is better). A typical crystallographic model based on 2.0 Å data has a coordinate error of less than 0.2 Å<ref>[http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html Garib N. Murshudov and Eleanor J. Dodson, Simplified error estimation a la Cruickshank in macromolecular crystallography, CCP4 Newsletter, January, 1997.]</ref>. | |||
See also [[Temperature_value#B-factors_and_coordinate_error|B factors and coordinate error]]. | |||
==Determination of Resolution== | ==Determination of Resolution== | ||
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==See Also== | ==See Also== | ||
Within Proteopedia: | Within Proteopedia: | ||
*[[Cryo-EM#Resolution]] | |||
*[[Temperature_value#Missing_Residues_and_Atoms|Missing Residues and Atoms]] | |||
*[[Temperature value]] | |||
*[[Temperature_value#B-factors_and_coordinate_error|B factors and coordinate error]] | |||
*[[X-ray crystallography]] | *[[X-ray crystallography]] | ||
*[[R value]] | *[[R value]] | ||
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External Resources: | External Resources: | ||
*[http://spdbv.vital-it.ch/TheMolecularLevel/ModQual/ A Glossary of Terms from Crystallography, NMR, and Homology Modeling] | *[http://spdbv.vital-it.ch/TheMolecularLevel/ModQual/ A Glossary of Terms from Crystallography, NMR, and Homology Modeling] | ||
*[https://en.wikipedia.org/wiki/Resolution_(electron_density) Resolution (electron density)] in Wikipedia. | |||
==Notes== | ==Notes== | ||
