The Z-values may be marginal, but of course you should inspect the
solution in Coot to see if the electron density makes sense, and the
packing of the protein molecules in the unit cell (look at symmetry
mates) is sensible. If this passes the sniff test, then you should clean
up your model (make it consistent with the target protein) and try to
refine it. If your target and model are really different in terms of
gaps, insertions, etc., and your electron density is good, this would be
a good opportunity to do some auto-building with Buccaneer based on your
initial phase solution, for example, to get to a better starting point
for refinement. If you can't refine the MR solution and drive R and
Rfree down significantly, you may still have some problems. With 70%
sequence identity, I would expect your model to be pretty close to your
target, and autobuilding may not be necessary to get to a good starting
point, although this can often save you some time.
_______________________________________
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: rrowl...@colgate.edu
On 1/28/2015 12:25 PM, jeorgemarley thomas wrote:
Hi, all
As per the suggestions, I hv done with the phaser MR and the solution
has come with screw axes P 21 21 21. here I am attaching the output
text from Mr and sol file. So Now should I go ahead with this? Please
suggest.
Thank you very much in advance !
On Tue, Jan 27, 2015 at 9:33 PM, jeorgemarley thomas
<kirtswab...@gmail.com <mailto:kirtswab...@gmail.com>> wrote:
Thank you so much to all for your kind concern.
Jeorge
On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs
<kay.diederi...@uni-konstanz.de
<mailto:kay.diederi...@uni-konstanz.de>> wrote:
Dear Jeorge,
you'll find some information about this in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
. A practical and easy way is described in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless
HTH,
Kay
On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene
<t...@shelx.uni-ac.gwdg.de <mailto:t...@shelx.uni-ac.gwdg.de>> wrote:
>Dear Jeorge,
>
>XDS make no claim to determine the SPACE GROUP but rather the
LAUE
>GROUP, as only the latter is taken into account during data
integration.
>
>This is definitely so during the indexing step (IDXREF.LP),
but even in
>CORRECT, when systematic absences are sometimes indicated,
XDS does not
>really choose the space group.
>
>Best,
>Tim
>
>On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
>> Hello Dr. Randy
>> Here is the IDXREF.LP I got in which, on the basis of
quality of fit, I
>> went for this space group well I would also try for the
other screw axes.
>> So should I Integrate the data from beginning with all
possible screw axes
>> of orthogonal space group? I am attaching the IDXREF.LP
screen shot here.
>>
>> Jeorge
>>
>> On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett
<rrowl...@colgate.edu <mailto:rrowl...@colgate.edu>> wrote:
>>
>>> Did you search all 8 possibilities of screw axes, e.g.
P2221, P21212,
>>> P212121, etc?
>>>
>>> Roger Rowlett
>>> On Jan 25, 2015 4:50 AM, "jeorgemarley thomas"
<kirtswab...@gmail.com <mailto:kirtswab...@gmail.com>>
>>> wrote:
>>>
>>>> Hi, I have processed the data using XDS and space group
found to be P 2 2
>>>> 2 (16) and I used the phaser MR for first phase
determination. The model I
>>>> have used has has more than 70 % sequence identity, when
I run the phaser I
>>>> got the message which I have attached here. And only sum.
file I got as an
>>>> output. Does any one have suggestion what should I do ? I
would highly
>>>> appreciate your kind suggestions. Thank you in advance.
>>>>
>>>>
>>>>
>>
>
>--
>Dr Tim Gruene
>Institut fuer anorganische Chemie
>Tammannstr. 4
>D-37077 Goettingen
>
>GPG Key ID = A46BEE1A
>
>
