Talk:Resolution: Difference between revisions
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==Proposed revision V2== | |||
In structure determinations, resolution is the distance corresponding to the smallest observable feature, i.e. if two objects are closer than this distance, they appear as one combined blob rather than two separate objects. For example, because the resolution of the light microscope is limited to roughly the wave length of light (400 nm = 4000 Å), it is not possible to resolve ("see") separate atoms under a microscope (atomic distances are on the order of 1 Å). The resolution of X-ray crystallography is theoretically limited by the wave length of X-rays (also on the order of 1 Å), but in practice, the quality of the available crystals determines resolution. High numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution. A structure determined using data to 1.5 Å would be referred to as a "1.5 Å structure". 2.05 Å is the median resolution for X-ray crystallographic results in the Protein Data Bank (88,701 on May 15, 2014). | |||
==Confusion of high vs. low resolution== | ==Confusion of high vs. low resolution== | ||
High resolution is characterized by being able to distinguish smaller features, so there is an inverse relationship between the quality of a structure and the length scale given for the resolution. For example, a 1.0 | High resolution is characterized by being able to distinguish smaller features, so there is an inverse relationship between the quality of a structure and the length scale given for the resolution. For example, a 1.0 Å structure resolves finer detail than a 4.0 Å structure, so the 1.0 Å structure is said to have higher resolution than the 4.0 Å structure. For non-experts, it would be less confusing if the terms were fine and rough resolution rather than high and low resolution, but high and low are the established terms in the field. | ||
==Resolution of a reflection vs resolution of a diffraction data set== | ==Resolution of a reflection vs resolution of a diffraction data set== | ||
Each diffraction spot (i.e. reflection) in a diffraction pattern has a nominal resolution. The higher the diffraction angle (i.e. further from the center of the diffraction image where the incoming X-ray beam would hit), the higher the resolution. In a diffraction experiment, the goal is to collect as many reflections as possible. However, reflections of high resolution are more difficult to measure because the intensity of reflections drops off at higher diffraction angles (and with that, higher resolution). In a diffraction image, you will see high intensity spots near the center, and more and more faded spots as you move away from the center. The overall resolution of a diffraction data set refers to the resolution range of reflections measured. For example, "data were collected from 20.0 | Each diffraction spot (i.e. reflection) in a diffraction pattern has a nominal resolution. The higher the diffraction angle (i.e. further from the center of the diffraction image where the incoming X-ray beam would hit), the higher the resolution. In a diffraction experiment, the goal is to collect as many reflections as possible. However, reflections of high resolution are more difficult to measure because the intensity of reflections drops off at higher diffraction angles (and with that, higher resolution). In a diffraction image, you will see high intensity spots near the center, and more and more faded spots as you move away from the center. The overall resolution of a diffraction data set refers to the resolution range of reflections measured. For example, "data were collected from 20.0 Å to 2.3 Å with an overall completeness of 96.5%" means that most reflections in this range were collected, and the data set would be described in brief as "2.3 Å resolution" data set, referring to the high resolution limit of the data collection. | ||
==Resolution and crystal quality == | ==Resolution and crystal quality == | ||
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==Resolution and diffraction data quality== | ==Resolution and diffraction data quality== | ||
A well diffracting crystal will yield a high resolution diffraction data. The higher the resolution, the more reflections in the data set. The number of reflections increases with the inverse cube of the resolution, so a 1.0 | A well diffracting crystal will yield a high resolution diffraction data. The higher the resolution, the more reflections in the data set. The number of reflections increases with the inverse cube of the resolution, so a 1.0 Å data set has '''eight''' times the number of reflections than a 2.0 Å data set. If you compare a given reflection measured on a well diffracting crystal to one measured on a poorly diffracting crystal, the former will be measured with higher precision (lower error). | ||
==Resolution and structure quality== | ==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 | 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. (http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html) | ||
==B-factors and coordinate error== | ==B-factors and coordinate error== | ||
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After an [[electron density map]] is calculated and refined with a fitted atomic model, an uncertainty of atomic position is calculated for each atom in the model. These single-atom uncertainties are called the B factors or temperature values of the atoms (see [[Temperature]]). | After an [[electron density map]] is calculated and refined with a fitted atomic model, an uncertainty of atomic position is calculated for each atom in the model. These single-atom uncertainties are called the B factors or temperature values of the atoms (see [[Temperature]]). | ||
==Determination of Resolution== | ==Determination of Resolution== | ||
