[phenixbb] coot links on Mac -> Possible MR solution

shuchi moni shuchixray at gmail.com
Mon Aug 2 02:19:50 PDT 2010

fred ya i got the solution with phaser with proper packing .
Space group P 6122
TFZ- 18.0
RFZ -7.8
PAK -1
LLG -282.453

density is clear and most of bulky residues are in side the density too .
but while running the refinement R factor is not going down. i am trying to
do fitting of the structure .

vandana kukshal

On Mon, Aug 2, 2010 at 2:27 PM, Vellieux Frederic
<Frederic.Vellieux at ibs.fr>wrote:

> vandana wrote:
>> hello
>>  i have diffraction of a crystal showing Rmerge 50 % resolution 21- 3.5 A.
>> this is due to crystal decay with time while data collection . multiplicilty
>> is 11 .0  and data is 99.6 % complete . i want to know that is this a good
>> data to solve structure with MR . i got solution with this data but the R
>> factor is 46.5 and R free is 51.4 .
>>  i want to know that if R merge is too high  we should proceed to solve
>> structure or not .
> Hi,
> From "X-ray structure determination, a practical guide" (Stout, G.H. &
> Jensen, L.H. citing Wilson A.J.C. [1950], Acta Cryst. 3, 397), the expected
> R-factors for the atoms of the structure randomly distributed in the unit
> cell (or asymmetric unit) are 0.83 for centric reflections and 0.59 for
> acentric reflections.
> The values you indicate are well below the figures mentioned above, so they
> indicate that what you have is not random. But this is not sufficient to
> tell you if what you have is a proper MR solution or not:
> What about the packing in the unit cell? Do you have crystal-forming
> contacts in the 3 directions of space that explain the formation of the
> crystal? If there are voids, there might be molecule(s) missing. What is the
> value of the Z-score provided by Phaser (if you have used Phaser)? In the
> resulting electron density map, do you see electron density that correspond
> to the "mutations" you have to carry out in order to go from model to target
> structure? If you see such electron density, then it is very likely that you
> indeed have a molecular replacement solution.
> The value of the Rmerge (you probably mean Rsym) you give (0.5) will
> probably not satisfy referees for a publication. What can always be done is
> to use several crystals for data collection, starting data collection at
> different (unique) positions, and merge the resulting data (restricting the
> data processing to the frames where the value of Rsym is acceptable). You
> should then end up with a merged data set that has a lower Rmerge value. We
> used to do this all the time in the days prior to cryo-cooling of crystals,
> when crystals were mounted in capillaries. Rmerge values of 10 to 15 % were
> typical then. That is if the value of the Rsym is indeed due to decay. High
> Rsym values are also obtained in cases of crystal twinning - without proper
> treatment- , improper space group assignment (although in that case, much
> much higher values are usually observed).
> Fred.
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