What is b-factor in cryo-EM?
In cryo-EM, the most widely applied method is a structure factor modification based on the Guinier plot, also known as B-factor correction (Rosenthal and Henderson, 2003).
What is EM map?
An EM map is represented by a set of unit vectors computed with the mean shift algorithm (see the “Methods” section). The voxel spacing of the maps is set to 7 Å. This vector representation originates from the approach used in MAINMAST, a de novo protein structure modeling method for cryo-EM maps23,24.
What is b-factor in crystallography?
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic displacement parameter, is used in protein crystallography to describe the attenuation of X-ray or neutron scattering caused by thermal motion.
What is cryo-EM structure?
Single-particle cryo-electron microscopy (cryo-EM), is an increasingly popular technique used by structural biologists to solve structures at atomic resolution. This technique complements x-ray crystallography because it reveals structural details without the need for a crystalline specimen.
What is a cryo-EM density map?
Abstract. High Resolution Image. The rigid-body fitting of predicted structural models into cryo-electron microscopy (cryo-EM) density maps is a necessary procedure for density map-guided protein structure determination and prediction.
What does B factor tell you?
The term B-factor, sometimes called the Debye-Waller factor, temperature factor, or atomic displacement parameter, is used in protein crystallography to describe the attenuation of X-ray or neutron scattering caused by thermal motion.
Why is cryo-EM better than EM?
A major advantage of cryo-EM over x-ray crystallography is that the molecule of interest does not have to be crystallised. Some proteins or important macromolecules simply can not be crystallised; others have their structures irreversibly changed by crystallisation.
What is cryo-EM good for?
These are used to reconstruct the 3D shape, or structure, of the molecule. Such structures are useful for uncovering how proteins work, how they malfunction in disease and how to target them with drugs.
What is normalized B factor?
Normalized B-factor measurements are utilized to compare motion across multiple structures. Normalized B-factor (B′) is an expression of the B-factor (B) in units of standard deviation (σB) about the mean value (μB, eq 1). This value is calculated across all heavy atoms in a protein–ligand complex crystal structure.
What is high B factor?
In the 3 to 5 angstrom resolution range, isotropic atomic B-factors can be 100, 200 or greater. At higher resolution, B-factors from 20-100 are reasonable.
How is B-factor sharpening implemented in locscale?
Local B-factor sharpening based on Guinier fitting Request a detailed protocol Map sharpening by local B-factor estimation from Guinier fitting was implemented in LOCSCALE using the same rolling density window framework described above. In this case two unfiltered half maps are provided as input.
What is resolution-dependent sharpening factor?
Resolution-dependent sharpening factor with three parameters. First the resolution-dependence of the map is removed by normalizing the amplitudes. Then a scale factor S is to the data, where log10 (S) is determined by coefficients b [0],b [1],b [2] and a resolution d_cut (typically d_cut is the nominal resolution of the map).
Are Atomic B-factors required for optimal sharpening?
Atomic B-factors are required for optimal sharpening Coordinate perturbations of the reference did not result in appearance or disappearance of features in the sharpened map, whereas coordinate randomization beyond a certain r.m.s.d. resulted in suboptimal sharpening.
Is global B-factor-based sharpening adequate for high-resolution density maps?
Clearly, even for this ‘stable’ specimen, a global B-factor-based sharpening method would not be adequate to correctly analyze the density map corresponding to these lower resolution regions ( Fig. 4B ). Fig. 4. MonoRes results and sharpened maps of T. acidophilum 20S proteasome (EMD-6287).