I have 144 diffraction images for a crystal of high mosaicity about 2 and low resolution about 3.14.
the crystal has been prepared and soaked with ligand. I would like to solve the crystal structure looking merely for a substrate binding site.
I tried using IMosflm, however the results of integration showed that all reflections are partial and there is no full reflection at all.
Then I used scala from CCP4 to do 2D integration for partial reflections, then check the density map using molecular replacement (protein has been deposited in PDB) with Phoenix. I can Max have LLG 900 and TFZ of 11. I can only recognize coarse features like helices, however the map is not clear for many side chains as well as at the binding site.
Any suggestion to improve the results using parameters adjustment of iMosflm, Scala, Phoenix MR. OR even new suggested software.
I appreciate any suggestion.
thanks
XDS provides "accurate" data for problematic data frames. As mentioned above, partials are not problematic.
My "best" experience with problematic data was the characterisation of the first crystals of trypanosomal pyruvate phosphate dikinase. The crystals had the bad habit of growing under the surface of a "protein-skin", located at the droplet surface. Before I had learned to dissect this skin away, the first crystal came out surrounded with this skin material. A few frames were collected on a home source for crystal characterisation. All data processing software failed to provide the correct Bravais lattice (very noisy data frames) but for XDS that gave orthorhombic right away.
So if you suspect your data frames not to be the "best you could ever have" I'd try to process the data with XDS. Getting the best processed data set will help you on your way to solve the 3D structure. And (as mentioned above) if your data turns out to be of insufficient quality, then you should go back to the bench to improve crystal quality and handle the crystals well for other sessions of data processing.
Mohammed,
could you please attach one picture of a diffraction image (e.g. as .jpg) ?
Thanks,
S.
Hi Mohammed,
I totally agree with Jonathan. Partial reflections are not the problem. The problems are probably due to bad quality of diffraction. For the data process, you may also try HKL2000.
Ps. Just a reminder, you may know it, make sure to select a correct space group when you process data, check it with Pointless. Sometimes you can get a MR solution with a low symmetry/accurate space group, but it can't be refined.
Good luck!
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