Dear All,
I have few basic questions for which I need help. I have a
3.4 A data and I have processed it to P4.
1.
I used pointless to find SG, it suggests P41 21
2. But I see two strong intensities in systematic absences
Intensities of systematic absences
h k l
Intensity Sigma I/Sigma
0 0
2 -0.7 0.3
-2.0
0 0
3 1.0 0.4
2.3
0 0
5 0.3 0.7
0.4
0 0
6 -0.7 0.9
-0.8
0 0
7 -0.4 0.9
-0.4
0 0
9 -0.2 0.9
-0.2
0 0
10 1.3 1.2
1.1
0 0
11 -0.8 2.1
-0.4
0 0
13 1.2 2.1
0.6
0 0
14 2.3 1.8
1.3
0 0
15 -1.0 1.9
-0.5
0 0
17 2.4 2.0
1.2
0
0 18 21.1
4.5 4.7
0
0 19 90.2
6.0 15.0
3 0
0 -0.1 0.2
-0.8
5 0
0 0.2 0.2
0.9
7 0
0 -0.3 0.2
-1.3
9 0
0 0.0 0.5
0.0
11 0
0 -0.2 0.6
-0.4
13 0
0 0.8 0.7
1.1
15 0
0 -1.2 0.6
-1.9
17 0
0 -0.3 0.8
-0.4
19 0
0 -1.4 0.6
-2.6
21 0
0 -2.2 1.2
-1.9
23 0 0
-0.8 1.3 -0.6
25 0
0 -1.2 1.1
-1.1
27 0
0 -0.9 1.6
-0.5
29 0
0 -0.4 1.7
-0.2
31 0
0 -7.1 1.3
-5.3
33 0
0 -2.4 2.1
-1.1
2.
When I used phaser for MR, it gave weak solution in p43, so I
scaled data in p43 21 2 (this also two intesities high like above in systamatic
absences) and used for Phaser to get the following solution
SINGLE solution
SOLU SET
RFZ=4.5 TFZ=9.4 PAK=0 LLG=105 TFZ==10.1 RF++ TFZ=17.7 PAK=0 LLG=282 TFZ==15.6
LLG=285 TFZ==12.4
SOLU SPAC P 43 21 2
SOLU 6DIM ENSE ensemble1 EULER 153.1 50.3
73.2 FRAC -0.11 0.03 -0.94 BFAC -2.65
SOLU 6DIM ENSE ensemble1 EULER 148.4 129.9
252.8 FRAC -0.32 -0.35 1.07 BFAC 4.01
Ensemble ensemble1 RMS variance(s): 1.13
3. I used this solution to further
refine the model in refmac, using local ncs, with/without jelly, optimized
weight/weight of 0.03, map sharpening with B=20 in several rounds.
I noticed that R factor R factor stayed around 33% while R free keeps
floating around 42%. I could see some density for missing loop in the model and
I could build but the R work and R free moving apart. By reading, I understand
that this is very common for low resolution data unless I use appropriate
restraints.
I am wondering if my space group is correct? I had understood that if it’s
right SG, high intensity reflections will not be found in systematic absences
but I started doubting if I have understood correctly.
This is my first low resolution
data, I want use this opportunity to learn refmac well. So could you please let
me know if my doubt is right regarding SG and how do
I troubleshoot.
Thanks
SDY
