When to do TLS refinement?

TLS refinement is generally valid at any resolution; at low resolution, it may be best to make each chain a single group, instead of trying to split them into smaller pieces. However, it is best to wait until near the end of refinement to add TLS; until then you should refine with isotropic ADPs only.

What is TLS refinement?

TLS refinement is designed to provide a simple description of anisotropic displacements when the resolution is not good enough to justify refinement of atomic ADPs.

What is NCS refinement?

Non-crystallographic symmetry (NCS) can (and in many cases should) be included in refinement. In CNS two models for NCS are available: Strict (constraints) – the model consists of a protomer. The relationships between protomers are fixed because the matrices do not change during refinement. …

What does a high B-factor mean?

In a high-quality model, B-factors reflect the mobility or flexibility of various parts of the molecule. High B-factors mean greater uncertainty about the actual atom position. Values of 60 or greater may imply disorder (for example, free movement of a side chain or alternative side-chain conformations).

What is real space refinement?

Such refinement is referred to as real-space refinement (RSR). In both cases the targets are the sums over a large number of similar terms corresponding to either reflections (FSR) or map grid points (RSR). In the case of cryo-EM an atomic model can also be refined using a reciprocal-space target.

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 a good B-factor?

B-factor is, in general, correlated with the resolution of your datasets. 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 is average B-factor?

B_max tend to increase if resolution decreases. 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).

How do you cite MolProbity?

Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21.

How is B-factor calculated?

For example: The temperature of the md simulation was set at 298K. The B-factor at 298 K was calculated from RMSF by the formula: B = 8*Pi*Pi*(RMSF)**2/3 . But the temperature in pdb file is 100 K.

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 does MolProbity score mean?

“[The MolProbity score] is a log-weighted combination of the clashscore, percentage Ramachandran not favored and percentage bad side-chain rotamers, giving one number that reflects the crystallographic resolution at which those values would be expected.

When do you use the term B factor?

Note that if the incident wave has wavelength In the context of protein structures, the term B-factor is used. The B-factor is defined as It is measured in units of Å 2 . The B-factors can be taken as indicating the relative vibrational motion of different parts of the structure.

Can a b factor be adjusted in ResearchGate?

Join ResearchGate to ask questions, get input, and advance your work. Although B-factor depends on resolution, however, it is not limited to the resolution of data. there are some other factors which also have effects on B-factor, such as radiation damage. You can adjust B-factor to some extent by varying different parameters and weight factors.

How is the B factor used in protein structure?

In the context of protein structures, the term B-factor is used. The B-factor is defined as It is measured in units of Å 2 . 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.

How is B factor related to data resolution?

B-factor is, in general, correlated with the resolution of your datasets. Lower resolution tends to correlate with high B-factor, which intuitively makes sense because greater molecular motions act to reduce resolution. I strongly advise against trying to refine to a target B-factor.