Anandhi, Assuming the data reduction went well, and you're in the right space goup, there could be a lot of model bias in your structure stemming from the starting model.
There are a lot of things to try. I would set all the B-factors to an artificially low B-factor to help de-mask errors. Then, you can generate a composite omit map and FEM maps to see if any obvious model errors show up in the electron density. After correcting these, you can try running Autobuild and PhaseAndBuild in Phenix. Compare all the models you get from each of these, especially in regions where your original model had high b-factors. Use Coot to identify areas of poor agreement with electron density and areas of poor geometry. Once you spent a while correcting the model, put it through one or more cycles of simulated annealing at different temperatures in parallel. Select several sets of coordinates that give the best Rfree convergence, and then subject those models to individual B-factor refinement. After that, check again in Coot for areas of high B-factors and areas of poor geometry (try especially to improve your Ramachandran Plot). Use MolProbity to help in identifying errors and clashes. If a few rounds of simulated annealing and model building don't improve things, try some refinement in CCP4 Refmac. PDB_REDO, which uses Refmac, can also help give you alternative models. While doing all these, don't be afraid to "cut-and-paste" regions from one model into another model and then correct the geometry in Coot. If B-factors don't come down no matter what you do, you could be in the wrong space group or have problems with the original data that need to be addressed. I hope this helps. Daniel ___________ Daniel M. Himmel, Ph. D. URL: http://www.DanielMHimmel.com/index_Xtal.html <http://www.danielmhimmel.com/> On Thu, Nov 8, 2018 at 7:41 PM Anandhi Anandan <anandhi.anan...@uwa.edu.au> wrote: > Hello everyone, > > > I am trying to solve the structure of a protein with a bound ligand at > 2.65 A resolution. XDS was used for data reduction, phaser-MR for molecular > replacement and Phenix for refinement. The refinement was done with the > default settings ( individual B factors, occupancy and TLS parameters). The > resultant atomic B factors are quite high. The overall B factor is 82 with > a minimum value of 34.57 and maximum of 225.13. I would like to know if any > of the data reduction parameters can affect the B factors and how best to > deal with this issue. > > > Anandhi > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
