1) do you have unexplained peaks in your native Patterson? (calculate
from your model and compare, if in doubt)
2) do you have both streaky and sharp reflections present on a subset
of your images ?
if answers to both questions are yes, then you might have a case of
LTD/OD twinning. The latest Acta Cryst D (Sept 2009) has three papers
dealing with such cases.
Looking at packing in your solution you should be able to figure out
the reason for the defect. Test as many crystals as possible: the
defect fraction is not the same in all crystals, so you might get one
with lower defect fraction!
good luck,
Peter
On 2 Sep 2009, at 17:48, Yuan Cheng wrote:
Eleanor Dodson wrote:
This phenonema doesnt necessarily mean you have lattice-tranlation
defects - pseudo translations are quite common with perfectly good
crystals.
Lattice translation defects usually imply your "crystal" has two or
more
layered different crystals in the beam.. It can be best detected by
an
analysis of the data statistics.
Eleanor
Yuan Cheng wrote:
Eleanor Dodson wrote:
You must have a pseudo translation vector of ~ 0.02 0.5 0.0
That relates solution 1 and 2, and 3 and 4.
That makes it hard to determine space group - there will be
absences
along 0k0 because of the translation so the space group could be
P 2i
2 2i or P2i 21 2i
But which ever SG it is thedata with k odd will be weak, and that
means you will have a higher R factor.
Eleanor
Jerry McCully wrote:
Dear all:
I am currently refining a structure solved by MAD and
somehow the R factor got stuck around 30% with 2.2 resolution.
There are four molecules in one ASU. Two had very good
density map and the other two were not equally good.
I tried using NCS during refinement but it did not help
much.
Then I checked my data. Actually I found that there are
alternate layers of strong and weak reflections. THe crystal is
in
a thin-plate shape with orthorombic space group.
Then I looked at my molecular replacement solution from Phaser
using my native data.
Actually phaser gave two sets of solutions, which showed
slightly different positions.
You can also see that there is a translation inside the same set
of
solution.
SOLU SET RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0
LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=46.1 PAK=0
LLG=4045
SOLU 6DIM ENSE ensemble1 EULER 184.052 0.185 175.770 FRAC
-0.49889 -0.00218 -0.00000
SOLU 6DIM ENSE ensemble1 EULER 225.116 0.167 134.696 FRAC
-0.47056 0.49706 0.00051
SOLU 6DIM ENSE ensemble1 EULER 359.333 31.677 180.633 FRAC
0.75769 -0.71475 -0.14004
SOLU 6DIM ENSE ensemble1 EULER 359.373 31.969 180.711 FRAC
0.73074 -0.21423 -0.14108
SOLU SET RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0
LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=47.3 PAK=0
LLG=4042
SOLU 6DIM ENSE ensemble1 EULER 213.115 0.173 146.741 FRAC
-0.49931 -0.00269 0.00045
SOLU 6DIM ENSE ensemble1 EULER 248.173 0.254 111.665 FRAC
-0.47091 0.49661 0.00101
SOLU 6DIM ENSE ensemble1 EULER 359.399 31.602 180.578 FRAC
0.75808 -0.71455 -0.13980
SOLU 6DIM ENSE ensemble1 EULER 359.378 31.255 180.361 FRAC
0.78370 -0.21555 -0.13830
I remember there is a discussion in CCP4bb about the same
topic
with the focus of pseudo-symmetry or translational pseudo-
symmetry.
Can anybody give some troubleshooting about my issue?
Thanks a lot and have a nice weekend,
Jerry McCully
_________________________________________________________________
Windows Live: Keep your friends up to date with what you do
online.
http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009
Hi Jerry,
I am having similar trouble with you. You might want to check out
this paper Acta Cryst.(2005) D61:67-74. It is about lattice-
tranlation
defects and how to correct it. Hopefull it is helpful!
Good Luck!
Yuan
Hi Eleanor,
Could you explain a little bit more about how to tell the
difference between pseudo-translational symmetry and lattice
translation
defects? Thanks a lot!
Yuan
