[phenixbb] Problem with molecular replacement

Shramana Chatterjee schatter90 at gmail.com
Thu Apr 9 09:06:18 PDT 2020

Thanks Roger.

I am trying through looking at packing of crystal lattice.It seems that
there are some gaps in the lattice. May be this is identical with the
solved one because of identical cell dimension and space group. Although I
think I should cross check with lattice as Matthew's analysis suggest a
different number of copies.

On Thu, Apr 9, 2020 at 8:51 AM Roger Rowlett <rrowlett at colgate.edu> wrote:

> For MR solutions with more than 4 molecules in the ASU, you can improve
> your chances of finding a solution by employing the following
> considerations:
> The number of protein units in the ASU predicted by Matthew's analysis my
> not be accurate for n>4. Always look at the molecular packing of potential
> solutions in the ASU using Coot or Pymol. You may discover you have too
> many molecules, and therefore overlaps, or too few molecules, leaving
> protein size gaps in the crystal lattice. Lattice packing of partial
> solutions may guide your thinking about the correct number of molecules in
> the ASU. A good solution should normally have symmetrical and clear solvent
> channels, and good contacts between all molecules.
> You may nave a better chance of obtaining a initial solution by searching
> with dimers (if structurally appropriate) than monomers.
> Unless your crystal form is identical to the solved version, there is no
> guarantee your N will be the same as the solved N molecules in the ASU. Use
> the Matthew's analysis and lattice packing as your guide.
> Using this approach I've been able to obtain MR solutions for ASUs with
> N=6-8, even with identities as low as 30%.
> Good luck.
> Roger Rowlett
> Gordon & Dorothy Kline Professor, Emeritus
> Colgate University
> On Wed, Apr 8, 2020, 11:43 PM Shramana Chatterjee <schatter90 at gmail.com>
> wrote:
>> Hi,
>> I am trying to solve a structure using a data solved by SAD as an
>> reference (ensemble in phaser). The structure I am trying to solve has 100%
>> sequence identity with the solved one. The problem that I am facing during
>> Phaser MR is that, in the solved structure there are 6 molecules in the ASU
>> although I am getting maximum 4 molecules in the ASU and also Rfree is
>> around 0.49 just after the phaser. Phaser is showing a good values of LLG
>> (>500) and TFZ (>8).
>> It would be very helpful if I get any suggestion about the
>> above-mentioned problem.
>> Thank you in advance.
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