It is not at all unusual for a biological homodimer to sit on a
crystallographic two-fold symmetry axis.  It is also not unusual
for such a dimer to sit entirely in the asymmetric unit.  This
cannot be used to identify the space group.

   The space group is determined by the diffraction data.  The
difference between C2221 and P212121 is that many of the reflections
predicted for P212121 have intensity equal to zero in C2221.  Since
you have a confusion between these two, I presume the P212121 model
has a pseudotranslational symmetry of (0.5,0.5,0.0).  This pseudo-
translational symmetry should be reported by xtriage, and will
mislead the twin detection tests.

   To determine which of these choices is the correct space group
you do not perform refinement, you look at the diffraction pattern
to see if there are non-zero intensities for the spots that must
be zero if the space group were C2221.  In P212121 with pseudo-C
centering these spots will be weak but observable.

   I am not surprised that your refinement in P212121 gives higher
R values than C2221.  In P212121 with pseudo-C symmetry half of
the reflections are weak and will have low signal/noise ratio.
With the assumption of C centering these weak reflections are
discarded and the R values will go down.  Your goal is not to
reduce the R values, but to fit the data.  If these reflections
have non-zero intensities you must integrate them and add them
to your refinement.

Dale Tronrud


On 12/01/10 08:31, Xiaopeng Hu wrote:
> Dear Dr. Kelly Daughtry,
> 
> Thanks for your help. The enzyme I am working on now functions as a dimmer and the active site is located at the interface. In previously published homology structures, there is one dimmer in the ASU and the dimmer has a tight NCS.  With C2221, the dimmer formed by symmetry mates fits the homology dimmer very very well. It is hard for me to understand how a enzyme can has such a crystallographic dimmer.
> 
> I am not good with Phenix, so I only tried xtriage to check the data set. With C2221, the twin test gives a good Z score which is much smaller than the critic 3.5, while with P212121, the Z score is high (>10). I didn't go further.
> 
> The maps look just the same between the two space groups.
> 
> ----- 原始邮件 ----- 发件人: "Kelly Daughtry" <[log in to unmask]> 收件人: "Xiaopeng Hu" <[log in to unmask]> 发送时间: 星期四, 2010年 12 月 02日 上午 12:05:08 主题: Re: [ccp4bb] Space group and R/Rfree value
> 
> Sorry, I meant with the P212121 refinement. You mentioned that it is probably twinned. Including the twin law in refinement with the P212121 data should help lower your R and Rfree values.
> 
> 
> If you have already included the twin law in your phenix refinement for the P212121 data, and R and Rfree can not be lowered, I would suggest that your data probably is C2221. Also, the fact that C2221 is not twinned while P212121 is twinned is an indicator to me that C2221 is probably correct as well.
> 
> 
> I wouldn't exclude C2221 as the real space group for not having the desired dimer. I have had tetrameric proteins crystallize with one mol / ASU, trimers with one mol/ ASU. If you turn on symmetry mates, do you see your intended dimer with the C2221 data?
> 
> 
> Last question/suggestion: Do the maps look the same between the two space groups? I would assume that the P212121 calculated maps are somewhat worse than the C2221 maps.
> 
> 
> With space group identity problems like these, you have to let the data tell you what is the correct space group. And from the looks of it, C2221 is the way to go.
> 
> 
> Best of luck, Kelly ******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *******************************************************
> 
> 
> 
> 2010/12/1 Xiaopeng Hu < [log in to unmask] >
> 
> 
> 1: No, the data reduction software didnt find twin and C2221 works well, so I never tried twin in refinement. 2: C2221 gives out a monomer in the ASU.
> 
> ----- 原始邮件 ----- 发件人: "Kelly Daughtry" < [log in to unmask] > 收件人: "Xiaopeng Hu" < [log in to unmask] > 发送时间: 星期三, 2010年 12 月 01日 下午 11:32:42 主题: Re: [ccp4bb] Space group and R/Rfree value
> 
> 
> 
> 
> Just to clarify, did you use the twin law in the phenix refinement? Also, is the C2221 solution a monomer or dimer in the ASU?
> 
> 
> 
> ******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *******************************************************
> 
> 
> 
> 2010/12/1 Xiaopeng Hu < [log in to unmask] >
> 
> 
> Dear all,
> 
> I am working on a data-set (2.3A) and the space group problem bothers me a lot.The space group of the data-set could be C2221 or P212121, since our protein functions as a dimer, and P212121 gives two molecular in the asym-uint, I think P212121 is more reasonable than C2221.However with C2221, I can refine the R/Rfree to 20/24 or lower, while with P212121 only to 26/30. Also Phenix points out that the crystal is probably a twin with P212121 but is OK with C2221.
> 
> I am not a real crystallographer, perhaps this problem is stupid, any help will be appreciated!!
> 
> Best wishes,
> 
> 
> Xiaopeng Hu
>