Re: [phenixbb] AutoSol with 4.2A dataset for a protein/DNA complex

I realized that I missed the fact that the P31 and P32 solutions yield very similar statistics - that's definitely not a good sign. I second Francis's suggestion for MR if there are any homologs, except I think you could use Phaser to go directly from the initial solution to Se phasing, and if you can actually find an MR solution it might work better to just start with the native data since it is potentially good enough to autobuild. -Nat On Thu, Feb 16, 2012 at 3:13 PM, Nathaniel Echols wrote:

On Thu, Feb 16, 2012 at 2:51 PM, Wei Shi wrote:

...

I processed the data with XDS in space group P31, and used *.cns.hkl file from XDSCONV as an input for AutoSol and also include the sequence for protein only.  The protein dimer has 418 residues and DNA is 32bp. I run Autosol with the default setting. Below is statistics I got. It seems that I didn’t get anything promising. Any comment or suggestion about what to try next? Thank you so much!

Statistics:

Top solution: 2           Sites: 11.                     Space group: P32.            FOM: 0.550.

BAYES-CC: 8.10.          Residues: 465           Side-chains: 0.             Chains: 60.

Model CC:  0.67           R-work: 0.4100          R-free: 0.4569.

At this resolution it's hard to know how much to trust those R-factors, and 60 chains is worrisome, but did you try running MR on the native dataset with the final model yet?  It may be too chopped up to be useful in a different crystal form, but if this works you're nearly there.

Other things to try: 1. Nucleic acids are much easier to see than protein at low resolution - see if you can find the double helix in the density-modified map.  (It will probably have protein residues built into it, but hopefully the shape is still distinctive.) 2. Generate an anomalous difference map in phenix.maps using the output model and either the peak or high remote (if you have it) wavelength (you might first need to combine the R-free flags generated by AutoSol with the original anomalous data) and look for clear Se peaks around the heavy atom sites.  Also check that the Se sites look like they're plausibly attached to Met residues. 3. Run phenix.find_helices_strands with the final map, and see how that works for MR on the native data.

-Nat