I have managed to solve the structure of a protein for which X ray diffraction data was collected and using a template structure, which was only missing 13 amino acids from the N terminal side, molecular replacement was done. the new model I obtained from Phaser (Phenix) does not have electron density for the extra 13 amino acid. TFZ and LLG scores are 40.0 and 1508 respectively
I was wondering whether the solution obtained after the Phaser is correct or no?
Also how to build the 13 amino acids?
whether their are any automated tools to assist in this building
I am not experienced with building model of protein derived from X-ray diffraction data. Nevertheless I suggest you to contact Prof. Mariusz Jaskólski.
e-mail: [email protected]
telefon: +48 61 829 1274
pokój: 4.103
strona www: www.man.poznan.pl/CBB/mariuszj.html
Dear Pankaj
You do not see the thirteen amino acids of the N terminal simply because they are very mobile and fluctuating, so to speak, that is probably an intrinsically disordered region. I think that the model you have, by using the PHENIX graphical interface and by running the Phaser-MR GUI, is correct. You can also check if the amino acids that make up it are the typical ones of the IDPs. To point out that the terminal tail is mobile you can build it with a modeling program and then you must use a molecular dynamics package (e.g. Gromax is a molecular dynamics package free on line ) to highlight the moving parts of your structure.
good work
Dear Pankaj :
From your post I assume that you have used as a search model for the molecular replacement the coordinates of the structure of your protein with the 13 amino acids from the N terminal missing, that you see some electron density in the area where these missing residues are expected to be located and that you need support to include them in your model. Otherwise (i.e. there is no electron density for those residues), Giovanni gave you the answer.
A very critical point is the kind of electron density map that you are using: these 13 missing residues are expected to show some electron density in the Fo-Fc-type map that should be contoured at 3-sigma (or even higher) to discard noise from signal.
There exists software that may help you in the model building of this missing residues. I use an obsolete version of Xtalview (http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html), but you may tray Coot (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/) or ARP/wARP (http://www.embl-hamburg.de/ARP/) that are available for research.
Good luck
I thank you all for the suggestions, especially to F. Javier Lopez-Jaramillo, who gave me clear idea about the 2 possibilities i can face. I have began to build the model on COOT itself.
Thank you once again
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