Dear SDY,
 
It is impossible to deduct from data statistics alone the difference between e.g. P43 21 2 and P41 21 2. Also with weak data like you have, a lot of artifacts may arise due to (weak) ice rings, intensity from neighboring strong reflections getting into the integration boxes of weak reflections, spurious reflections due to contaminating salt microcrystals etc.etc.etc.
 
What you need to do is to integrate your data in the basic point group: P4 or P422, depending how sure you are about the additional twofold, and then run Phaser with the SGALTERNATIVE ALL option, so it will check all possible space groups (P41 2 2, P41 21 2, P42 2 2, P42 21 2 etc.). I am pretty sure you will find that the space group which will come out then will not be the P43 21 2 you have assumed right now and that refinement in this space group will solve your problem. Since with your current solution, you will have most of your symmetries correct, you still can get Rfactors in the 30-40% range like you observe. If you wish, after you found the correct space group with Phaser, you could reprocess your data using this correct space group.
 
Best regards,
Herman Schreuder
 
 
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of SD Y
Sent: Sunday, November 04, 2012 4:04 PM
To: [log in to unmask]
Subject: [ccp4bb] low-resolution data and SG

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.

<!--[if !supportLists]-->1.       <!--[endif]-->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

<!--[if !supportLists]-->2.       <!--[endif]-->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

<!--[if !supportLists]-->3.      <!--[endif]-->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