Am 20:59, schrieb Poul Nissen:
I very much agree - refinement will tell you if the high-res data make sense. Another very good test is the Wilson plot - it should look straight and reasonable. Inflated I/sigI values will not escape a strange appearance such as the WIlson plot flattening out at higher resolution. I normally find a very good consistency between the resolution cut-offs indicated by the wilson plot and the refinement statistics.
good advice
Poul On 22/04/2010, at 19.59, Edward A. Berry wrote:There are plenty of structures in the database with R-sym=0.99. But something is odd here. If I understand R-pim, it should always be bigger than Rsym, because this factor of sqrt(N/(N-1)) is always >1 Are you saying Rpim is .30 and Rsym is 1.00?
a correction: the factor of sqrt(N/(N-1)) that you quote is for R-rim (same as R_meas), not for R-pim.
R-pim (more or less same as R_mrgd-I) has a factor of sqrt(1/(N-1)) so a value of 30% is believable. As this is on intensities, the equivalent quantity calculated on amplitudes should be even less. That means that refinement should be happy with those data!
see the wiki: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors
HTH, Kay
Last time I deposited a structure, Rsym and Rmerge in the last shell are optional. I would leave it out and rely on the excellent I/sigI in the last shell, and use all the data (provided after refinement R-free in the last shell is < .4). Ed Daniel Bonsor wrote:Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
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