Ahh low resolution structure solution, my favorite! Your SKEW isn't very promising… usually scores of 0.1 and above are better. I bet the maps before DM and after DM look bad. Getting the SeMet substructure at 4.2A is challenging, extending the phases from 4.2 to 3.2 without a buildable model is going to be even more challenging. [1] Are there any endogenous anomalous scatterers? I'm thinking Zn since this is a DNA:protein interaction. If you have crystals, run a fluorescence scan at the Zn edge. [2] Do you have any structural information on the protein ? (perhaps the apo state has been solved) If the answers to [1] and [2] are yes, then you can use the protein as an MR to find the Zn site and cross validate with the SeMet data. (use the Zn phases to find SeMet) If the answer is no… there's still other options. F On Feb 16, 2012, at 3:51 PM, Wei Shi wrote:
Hi everyone,
I have got a 4.2A SeMet MAD dataset for a protein-DNA complex. And, the native dataset for this protein-DNA complex is ~3.2A. The space group for the native and SeMet crystals seem to be different. I am not sure whether it’s possible to solve the structure with the current data I have, and wondering whether any of you have experience with working with this low-resolution data and any suggestion for me.
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.
Under Heavy-atom search and phasing:
Space group
# of refined sites
FOM
Overall score
R-factor
Map skew
Corr. of local RMS density
Solution1
P31
11
0.530
8.10+/-11.80
0.4184
-0.12
0.66
Solution2
P32
11
0.550
8.10+/-11.80
0.3881
-0.10
0.66
Best, Wei
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--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder