Don't worry. High B-factor just means that the probability of the atoms being at the specified coordinate position is low, for whatever reason.
In most cases this is completely normal and often indicative of solvent exposed surface residues, and a look at the electron density will show whether this uncertainty is due to absence of electron density or a result of poor modeling. Remember that cranking up the B-factor is the 'emergency exit' for the refinement program if an atom is located at an incorrect coordinate position from which it cannot be expelled (due to stereochemical restraints). BR From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Arka Chakraborty Sent: Saturday, April 21, 2012 11:14 AM To: [email protected] Subject: [ccp4bb] high temp factor in coot! Hi all, I have solved the structure of a decamer dna oligonucleotide. Analysis in CCP4 using baverage shows acceptable(<30) avg b factors for all the residues. However temperature factor variance analysis option in coot gives a figure of 150 for one of the residues with a huge red bar. I would like to ask how should this be interpreted? What exactly does the bfactor plot in coot signify? Thanks in advance, ARKO -- ARKA CHAKRABORTY CAS in Crystallography and Biophysics University of Madras Chennai,India
