Hello,
The rmerge for my scaled data is 72% or 0.722 for outershell. I tried to refine using the same data set however the electron density doesn't look good. So what can be done to lower the rmerge?
I am using CCP4i/iMosflm for data reduction.
Dear Shubhashish Chakraborty ,
please check the following paper:
Article Assessing and maximizing data quality in macromolecular crys...
As you will read, Rmerge is a "flawed indicators that have been replaced by R meas. We recommend these be removed from all data reduction software".
So, the questions here are:
- what's the resolution of your dataset?
- how do the (other) overall statistics for your dataset look like? Rpim, Rmeas, I/sigI, CC1/2?
- how did you phase your structure? If MR, what's the TFZ and LLG scores? If experimental phasing, what CCanom, what ANOMcompleteness, what wavelength, what heavy-atom, what method (SAD, SIR, MIR), what program, what phasing power?
I apologise for so many questions, but these are rather important ones if you really want some feedback/input from the community. Only then, we might have a hint on what's the problem with your dataset (or data reduction protocol, or phasing protocol, or refinement protocol).
Best,
Jose
Jose A. Brito
So I had just reduced the resolution and now the rmerge obtained is much lower.
I have not added any heavy atom and I am using molecular replacement using phaser MR.
Dear Shubhashish Chakraborty ,
I apologise for the blunt approach, but you should not (you MUST NOT), use Rmerge to make such a decision.
Like I pointed out earlier, Rmerge is a flawed and outdated metric to use and make a decision on resolution limit. Just as an example, in the following paper I had an Rmerge for the outer shell of well above 280 % (yes, 280 %!!):
Article Electron Accepting Units of the Diheme Cytochrome c TsdA, a ...
If I followed your approach I would never have solved the structure.
If your completeness allows it, and your I/sigI is good enough, cut your resolution where CC1/2 > 30 %.
Nevertheless, you should check your MR solution. The "bad" electron density maps you have mentioned previously could be a result of a "marginal" solution.
Just my two cents....
HTH, best regards,
Jose
Shubhashish,
just one number does not tell anything.
If you have 0.72 in the last shell and you have 100% completeness and more than 10 times the redundancy, the last shell is fine. When one checks the quality of data, one has to check several parameters and have a whole picture.
You can not a get good data set from the bad diffracting crystal.
Did you check if you are using a high symmetry space group to merge the lower symmetry data?
Did you check if your crystal was dying? Maybe you have to remove frames from merging.
Best,
George.
George Minasov Thank you for your suggestion. Well, I did scale the data by increasing the resolution and further, I got the electron density as well have solved the structure.
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