(Off-list)
Dear Kay and Harry,
You mentioned difficult datasets being of interest for the ACA conference. I am not coming, but do have some interesting datasets, viz., many datasets of a particular crystal form of a calmodulin/peptide complex which have defied my [not exhaustive] attempts to solve them. I have a closely-related complex structure which was fairly easy to solve, so I am not so invested in working super hard at the difficult one, but all the same, would really like to see what it looks like. The crystals have calcium and sulfur atoms (some collected at 1.6, some at 1.0 Ang) and there is also the plethora of possible MR models in the pdb and my closely-related complex, in which calmodulin looks dissimilar from the other pdb cam structures, based on DALI. I think these particular datasets may be tetartohedrally twinned, but from the literature it seems this can be overcome by tweaking the right MR model, maybe using some anomalous, etc.
Interested? I would give you all the images, I guess, which would be ~10 sets of varying number of frames? Radiation damage appears to be of variable degree.
Jacob
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Kay Diederichs
Sent: Sunday, February 23, 2014 2:55 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] High Rwork/Rfree vs. Resolution
Projects and problems like this are clearly a justification for asking to deposit not only the results from data processing, but also the raw data frames. These would allow developers to improve the models underlying their algorithms, and to find those corner cases where the algorithms break. That would help everyone.
Maybe you could make this dataset (and sequence) available for the forthcoming IUCr conference, as an example for a difficult dataset? (send email to Ed Collins or me) You would profit from the fact that experienced crystallographers do their best to make the most of your data.
best,
Kay
On Fri, 21 Feb 2014 20:13:33 -0600, Chris Fage <[log in to unmask]> wrote:
>Thanks for the assistance, everyone.
>
>For those who suggested XDS: I forgot to mention that I have tried
>Mosfim, which is also better than spot fitting than HKL2000. How does
>XDS compare to Mosflm in this regard?
>
>I am not refining the high R-factor structure with NCS options. Also,
>my unit cell dimensions are 41.74 A, 69.27 A, and 83.56 A, so there
>isn't one particularly long axis.
>
>I'm guessing the low completeness of the 1.65 angstrom dataset has to
>do with obstacles the processing software encountered on a sizable
>wedge of frames (there were swaths of in red in HKL2000). I'm not sure
>why this dataset in particular was less complete than the others.
>
>Thanks,
>Chris
>
>
>On Fri, Feb 21, 2014 at 6:41 PM, Chris Fage <[log in to unmask]> wrote:
>
>> Dear CCP4BB Users,
>>
>> I recently collected a number of datasets from plate-shaped crystals
>> that diffracted to 1.9-2.0 angstroms and yielded very nice electron
>> density maps. There is no major density unaccounted for by the model;
>> however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
>> ~0.30, respectively. Probably due to the more 2-dimensional nature of
>> my crystals, there is a range of phi angles in which the reflections
>> are smeared, and I am wondering if the problem lies therein.
>>
>> I would be grateful if anyone could provide advice for improving my
>> refinement statistics, as I was under the impression that the
>> R-factors should be ~5% lower for the given resolution.
>>
>> A few more pieces of information:
>> -Space group = P21, with 2 monomers per asymmetric unit; -Chi square
>> = 1.0-1.5; -Rmerge = 0.10-0.15; -Data were processed in HKL2000 and
>> refined in Refmac5 and/or phenix.refine; -PHENIX Xtriage does not
>> detect twinning, but hints at possible weak translational
>> pseudosymmetry; -I was previously able to grow one atypically thick
>> crystal which diffracted to 1.65 angstroms with Rwork/Rfree at
>> 0.18/0.22.
>> Unfortunately, the completeness of the dataset was only ~90%.
>>
>> Regards,
>> Chris
>>
>
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