As Eleanor says, errors in an electron density map tend to accumulate on special positions, i.e. on rotation axes (there are plenty of them in F432). There are statistical reason for this and the effect is often observed in small molecule crystallography. In such cases attempts to put atoms (e.g. water) on the noise peaks and refine their occupancies leads to very small values. Missing data can make this problem more severe!
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 6 Jan 2010, Eleanor Dodson wrote: > The obvious Q is whether there is some additive in the crystallisation or cryo > which could be showing up in the maps.. > > But in such a high symmetry space group is it possible that the blobs are on > some symmetry axis? I sometimes observe awful holes or peaks on 3 fold axes, > where I think any "noise" feature isexaggerated by the symmetry. > > Eleanor > > > > Rajan wrote: > > Dear All, > > > > Happy New Year > > > > I am working with a 2.06 Ang resolution structure in F432 space group and > > further using REFMAC (also tried Phenix) program for refinement of my > > model. > > > > Every thing in the structure seems good, R factor/ R free= 18.59/20.77 but > > the structure is too noisy (blobs of difference Fourier with red as well as > > green density). > > > > As such electron density is looking good for the protein part. > > > > Is there any parameter which i had to check. > > > > Thanking you in advance > > > > Rajan > > > >
