What is B-factor in PDB file?
The B-factor describes the displacement of the atomic positions from an average (mean) value (mean-square displacement). Higher flexibility results in larger displacements, and eventually lower electron density.
What is a good 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.
What are B-factor values?
In contrast, the temperature value (also called temperature factor or B factor) quantitates the uncertainty for each atom. At typical resolutions for protein crystals (where occupancy cannot be distinguished from B value), a high temperature factor reflects a low empirical electron density for the atom, and vice versa.
How is B-factor calculated?
The B-factor at 298 K was calculated from RMSF by the formula: B = 8*Pi*Pi*(RMSF)**2/3 .
What is average B-factor?
In the highest resolution range (0.0–1.5 Å) and when all the atom types are considered together, the average B-factor at pcVol = 100% is only 25 Å2, while it is 80 Å2, in the lowest resolution range (3.3–4.0 Å).
What does PDB file contains?
A PDB file is typically created from source files during compilation. It stores a list of all symbols in a module with their addresses and possibly the name of the file and the line on which the symbol was declared. This symbol information is not stored in the module itself, because it takes up a lot of space.
What does B-factor tell you?
The B-factors can be taken as indicating the relative vibrational motion of different parts of the structure. Atoms with low B-factors belong to a part of the structure that is well ordered. Atoms with large B-factors generally belong to part of the structure that is very flexible.
What is anisotropic B-factor?
An anisotropic scale factor is a multiplicative factor like the overall B-factor. Like the overall B-factor, its value varies with resolution. But, unlike the overall B-factor, its value also varies with direction.
What is B-factor analysis?
B-factors, also known as temperature factors or atomic displacement parameters, are calculated parameters in X-ray crystal structures that reflect disorder of atoms from their ideal equilibrium positions due to both thermal motion and positional disorder.
What is the use of PDB?
Program database (PDB) is a proprietary file format (developed by Microsoft) for storing debugging information about a program (or, commonly, program modules such as a DLL or EXE). PDB files commonly have a . pdb extension. A PDB file is typically created from source files during compilation.
What are B factors in Pymol?
B-factors indicates the mobility (displacement) of the atoms. This displacement may be because of temperature-dependent vibrations or static disorder in a crystal lattice. Displacement has a direct relationship with flexibility i.e. more flexibility in the atom, larger will be the displacement or more will be B-factor.