[phenixbb] Asymmetric unit content
tim.gruene at psi.ch
Mon Dec 12 08:06:01 PST 2016
7A could be sufficient to localise the Se-atoms from an anomalous difference
map, when the data are collected at or beyond the peak wavelength, provided
you can collect complete data.
Since you seem to have the crystal, and if you have access to some synchrotron
beamtime, go ahead and try.
On Monday, December 12, 2016 7:42:37 AM CET Sharan Karade wrote:
> Thank you for valuabla suggestions. I apologies for misleading information.
> I solved the structure at 2.8A (native) as powel got correctly.During data
> collection out of 50 2 crystals diffracted better dan 3A. But my guide want
> me to get setMet data, unfortuanately crystals poorely diffracting (7A) now
> which grown in same condition and also tried to play with condition to get
> better crystal but failed. Is there any way to prove that with data what i
> have. ?
> On Monday, December 12, 2016, Roger Rowlett <rrowlett at colgate.edu> wrote:
> > The Matthews coefficient is relatively efficient at distinguishing likely
> > ASU content for N<=4. However, the probability distribution of the
> > solvent
> > content of protein crystals is broad enough that it is difficult to
> > distinguish from the Matthews coefficient alone if an ASU has say, 4 or 6
> > (or 6 or 8) molecules in the ASU. Realistically, the Matthews coefficient
> > is going to give you a range of likely possibilities. 1 vs. 2 is easy to
> > distinguish. Not so 4 vs. 5 vs. 6.
> > Ultimately, you have to look at your MR solution and the molecule packing
> > in the unit cell. Said packing should make chemical sense, and reveal
> > highly symmetric solvent channels. A periodic "gap" in your crystal
> > packing, supported by un-filled electron density, is a clue that something
> > might be missing. At 7A resolution, I would suspect that the electron
> > density clarity would not be terrific.
> > 5 molecules in the ASU seems a bit odd to me. (4 or 6 seems more
> > probable.) If it is 5 molecules, one of the molecules would have to be on
> > a
> > symmetry axis, completing a "symmetry" dimer, with two other dimers in the
> > ASU? I've seen 6 molecules in the ASU in C2, with one tetramer and one
> > half-tetramer on the symmetry axis. When solving that one, the Matthews
> > Probability calculator insisted that there were 4 molecules in the ASU.
> > Turned out to be 6. I initially placed 4 molecules in the ASU, and saw a
> > clear crystal-packing gap for another dimer that would fit neatly next to
> > the symmetry axis.
> > _______________________________________
> > Roger S. Rowlett
> > Gordon & Dorothy Kline Professor
> > Department of Chemistry
> > Colgate University
> > 13 Oak Drive
> > Hamilton, NY 13346
> > tel: (315)-228-7245
> > ofc: (315)-228-7395
> > fax: (315)-228-7935
> > email: rrowlett at colgate.edu
> > On 12/12/2016 9:52 AM, oleg at quantumbioinc.com wrote:
> >> Compute Matthews coefficient.
> >> e.g. using
> >> http://www.ruppweb.org/mattprob/default.html
> >> Oleg
> >> -----Original Message-----
> >> From: "Sharan Karade" <sharankarade at gmail.com>
> >> Sent: Sunday, December 11, 2016 6:05am
> >> To: phenixbb at phenix-online.org
> >> Subject: [phenixbb] Asymmetric unit content
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >> Unsubscribe: phenixbb-leave at phenix-online.orgDear all,
> >> I have solved the structure in C121 space group, having five
> >> molecules in asymmetric unit, my supervisor have doubt about the fifth
> >> molecule becoz of poor density fit, if i delete the fifth molecule, there
> >> is a space for the molecule and crystal is not continuous, i calculated
> >> difference map from Phenix by deleting fifth molecule and got the Map
> >> showing presence of molecule. My supervisor want me to get SetMet data,
> >> but
> >> crystals are diffracting poor (7A). Is there any way to convince my
> >> guide.
> >> advance thanks for valuable suggestions.
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