Hello,
Here we deal with symmetry and the unique part of reciprocal space (the
reciprocal space "asymmetric unit" so to speak).
C222(1) has eight asymmetric units (international tables, space group 20);
P2(1) only has two. Assuming that Friedel's law does apply, then the
minimum rotation range to collect a non-redundant data set (one
observation per reflection) is 90 degrees, provided that the crystal is
"correctly" and perfectly aligned. Normally with our current data
collection methods where the crystal is randomly oriented, we would
collect more than 90 degrees (180 degrees, or 360 degrees with the
Pilatus detectors on an intense SR beamline where you cannot really
check during data collection how well the crystal fares during exposure
to the X-rays - "shoot first, think later".
The "reciprocal space" asymmetric unit in C222(1) is smaller.
I assume that what you are doing is to take the reduced data set file
(an MTZ file probably) and reduce the symmetry from C222(1) to P2(1).
You will not cover the monoclinic reciprocal space asymmetric unit by
doing so.
The way to do it is to take the file from processing, before
(crystallographic symmetry) merging of the equivalents, and perform the
scaling and merging in the P2(1) space group. Or reprocess the data
frames in P2(1) if you have lost the unmerged data file.
Now of course this will still give you a poor completeness if you have
used a strategy to optimize data collection in the orthorhombic space
group (you won't have collected enough data then for good completeness
in the monoclinic space group).
I hope this is clear !
HTH,
Fred.
On 24/03/13 11:20, Appu kumar wrote:
I run the phenix.xtriage to evaluate the twining but it suggest no
twining. When i reindex from C2221 to P21, the completeness of data
reduced from 95 % to 35% whereas the map is very good and Rwork and
Rfree are 26/31 for 2.2 resolution. I do not understand why the
completeness of data reduced so much on reindexing. please Can anyone
explain this phenomenon.
Thank you
On 24 March 2013 13:30, Matthias Zebisch
<matthias.zebi...@bbz.uni-leipzig.de
<mailto:matthias.zebi...@bbz.uni-leipzig.de>> wrote:
the p21 c2221 ambivalence can mean severe twinning (i had a
similar case just now - try several crystals from the same
condition) !
What do the twinning statistics suggest?
cheers, Matthias
-----------------------------------------
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Fax (+44) 1865 287547
emailmatth...@strubi.ox.ac.uk <mailto:matth...@strubi.ox.ac.uk>
Websitehttp://www.strubi.ox.ac.uk
-----------------------------------------
On 3/24/2013 7:46 AM, Appu kumar wrote:
Thank you for the quick reply. After molecular replacement , i
have done only few cycle of refinement in refmac. I have not done
any solvent modification or NCS averaging. I have initially
indexed the data in C2221 but Rfree was not decreasing so i
reindexed the data in data in P121 space group keeping the Rfree
flag of C2221. While analysing the symmetry mates , i found large
space but no density. structure of Ligand binding domain is
almost identical with 90% identity in sequence. I am stuck with
this problem and don't know how to process further.
Please give me your valuable suggestion. I will appreciate your
effort.
Thank you
Appu
On 24 March 2013 02:38, Raji Edayathumangalam <r...@brandeis.edu
<mailto:r...@brandeis.edu>> wrote:
Dear Appu,
I am not sure that I have a complete sense of the issue at
hand since some of the information needed to think your issue
through is missing in your email. For example, to what high
resolution cut-off were the data measured? What resolution
limits were used for the MR search? How do the unit cell
dimensions and space group in the two cases compare?
I am guessing the ligand binding domain in your protein has
the identical sequence to that of the published ligand
binding domain that you use as a template in your MR search.
In any case, here are a couple of my thoughts:
(1) It might be worth setting up different runs of MR with
different numbers for expected copies (not just two copies
but also one copy and three copies just in case you have one
of the extreme cases of solvent content)?
(2) If the MR solution is correct and there is physical room
for a DNA binding domain in your lattice (check by displaying
symmetry mates), perhaps the DNA binding domain is
disordered. In that case (and if all attempts with current
data fail), you may have to crystallize the protein in
presence of DNA.
Good luck!
Raji
On Sat, Mar 23, 2013 at 2:26 PM, Appu kumar
<appu.kum...@gmail.com <mailto:appu.kum...@gmail.com>> wrote:
Dear members,
I am doing a molecular
replacement of a transcription factor whose ligand
binding structure(24000 Da) is available in PDB but not
for the DNA binding(13000 Da). When i am searching for
the two copies from ligand binding domain as a template
model, i am getting very good solution but i am not
getting any density for the DNA binding domain to build
up in density. The space gorup is P 1 21 1 (4) and unit
cell parameters are Unit Cell: 57.43 69.36 105.99
90.00 90.00 90.00. Please guide me how to get the
complete model structure. Table below show the matthews
statistics
For estimated molecular weight
37000.
Nmol/asym Matthews Coeff %solvent P(2.20) P(tot)
_____________________________________________________________
1 5.71 78.46 0.00 0.01
2 2.85 56.91 0.62 0.70
3 1.90 35.37 0.37 0.29
4 1.43 13.82 0.00 0.00
_____________________________________________________________
The phaser molecular replacement gives the following table.
istogram of relative frequencies of VM values
----------------------------------------------
Frequency of most common VM value normalized to 1
VM values plotted in increments of 1/VM (0.02)
<--- relative frequency --->
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
| | | | | | | | | | |
10.00 -
8.33 -
7.14 -
6.25 -
5.56 -
5.00 -
4.55 -
4.17 -
3.85 --
3.57 ---
3.33 ------
3.12 ----------
2.94 **************** (COMPOSITION*1)
2.78 -----------------------
2.63 --------------------------------
2.50 -----------------------------------------
2.38 ------------------------------------------------
2.27 --------------------------------------------------
2.17 -----------------------------------------------
2.08 --------------------------------------
2.00 --------------------------
1.92 ---------------
1.85 -------
1.79 ---
1.72 -
1.67 -
1.61 -
1.56 -
1.52 -
1.47 * (COMPOSITION*2)
1.43 -
1.39 -
1.35 -
1.32 -
1.28 -
1.25 -
$TABLE : Cell Content Analysis:
$SCATTER
:N*Composition vs Probability:0|3x0|1:1,2:
$$
N*Composition Probability
$$ loggraph $$
1 0.306066
2 0.00141804
$$
Most probable VM for resolution = 2.27817
Most probable MW of protein in asu for resolution =
92664.2
Thank a lot in advance
--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University
--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494
