[ccp4bb] AW: [ccp4bb] Space group problem

@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Space group problem I thought there was a theoretical Rmeas number for I/sigma=2 that is around 50%? In my case, the Rmeas is much higher. Before, we reported P62(4) and got rejected. I'll just change a journal. Hopefully reviewer will not be too picky about

Re: [ccp4bb] Space group problem

Hi, please post the pointless table Analysing rotational symmetry in lattice group P 6/m m m. This gives a quite clear information about the presence/absence of rotational symmetry axes. Look at at the following example Analysing rotational symmetry in lattice group P 6/m m m

[ccp4bb] AW: [ccp4bb] Space group problem

: Mittwoch, 7. Mai 2014 19:26 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Space group problem Hi all, I have a 360 degree data set collect on home beam. I used XDS to integrate the frames in P1. I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the log below. The cell looks

Re: [ccp4bb] AW: [ccp4bb] Space group problem

-- -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Rain Field Gesendet: Mittwoch, 7. Mai 2014 19:26 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Space group problem Hi all, I have a 360 degree

[ccp4bb] Space group problem

Hi all, I have a 360 degree data set collect on home beam. I used XDS to integrate the frames in P1. I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the log below. The cell looks like P3 and pointless suggest P6. But the Rmerge and Rmeas are much higher than normal at

Re: [ccp4bb] Space group problem

additional info: If I let xds go through, it will choose P6. actually pointless suggest P62/P64. The thing is the Rmeas and Rmerge are significantly higher for P2/P3/P6 than P1, especially the highest shell. That indicates those higher symmetry ones are not the choice, it that right? (Actually,

Re: [ccp4bb] Space group problem

I thought there was a theoretical Rmeas number for I/sigma=2 that is around 50%? In my case, the Rmeas is much higher. Before, we reported P62(4) and got rejected. I'll just change a journal. Hopefully reviewer will not be too picky about that. Thanks to everyone!

Re: [ccp4bb] Space group problem

It is definitely P6something or P3something with a twinning about the unique axis. The differences in merging statistics between P2 P3 and P6 are not very significant in my opinion. On May 7, 2014, at 1:16 PM, Rain Field rainfiel...@163.com wrote: additional info: If I let xds go through,

Re: [ccp4bb] Space group problem

Hello Rain Field, I third Felix and Craig, there is nothing unusual about the statistics table you present. The data look pretty good and I would assume P6_something and integrate further than 3.1A. Regards, Tim On 05/07/2014 08:16 PM, Rain Field wrote: additional info: If I let xds go

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Space group problem?

, assessment of the diffraction pattern etc. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nazia Nasir Phd2009,ProteinCrystall.Lab Gesendet: Dienstag, 1. April 2014 20:00 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] Space group problem? Dear Jurgen

Re: [ccp4bb] Space group problem?

Dear Chen, how sure are you that your crystals contain the protein of interest? Repeatedly washing harversted crystals in crystal stabilization solution followed by SDS-PAGE coupled to appropriate staining protocols (e.g. Coomassie, Silver staining) or western blotting can give a pretty

Re: [ccp4bb] Space group problem?

Dear Savvas, Thank you for your reply and your nice protocol. I am also worried of this problem so I have already run my crystals on the gel for several times. The result is so clean that you can hardly draw any other conclusions except that the crystals are made up of the full-length molecule.

[ccp4bb] AW: [ccp4bb] Space group problem?

. März 2014 23:46 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Space group problem? Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment. Shelxd is able to locate 6 sites with a distinct CC and FOM

Re: [ccp4bb] AW: [ccp4bb] Space group problem?

*Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Chen Zhao *Gesendet:* Montag, 31. März 2014 23:46 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] Space group problem? Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6

Re: [ccp4bb] AW: [ccp4bb] Space group problem?

. März 2014 23:46 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] Space group problem? Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment. Shelxd is able to locate 6 sites with a distinct CC

Re: [ccp4bb] AW: [ccp4bb] Space group problem?

@JISCMAIL.AC.UK *Betreff:* [ccp4bb] Space group problem? Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment. Shelxd is able to locate 6 sites with a distinct CC and FOM. After density

[ccp4bb] Space group problem?

Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment. Shelxd is able to locate 6 sites with a distinct CC and FOM. After density modification in shelxe, the contrast of the two enantiomers is

Re: [ccp4bb] Space group problem?

BTW, I forgot to mention that phenix.autosol also gave similar result. On Mon, Mar 31, 2014 at 5:46 PM, Chen Zhao c.z...@yale.edu wrote: Dear all, I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A. It is hard to improve the derivative resolution at the moment.

[ccp4bb] space group problem

Hi all, We run into an interesting space group problem. The same diffraction image can be either indexed into space group C2, with a=145, b=44, c=67, and beta=110.5; or space group P2 (should be P21 after scaling), with a=67, b=44, c=136, and beta=96.8. Both are refined ok during index.

Re: [ccp4bb] space group problem

Dear Junyu, it looks to me like you encounter a classical monoclinic feature: one can index monoclinic always in two ways origin | V A' -- A \ /\

Re: [ccp4bb] space group problem

What is the Rmerge in each case? -James Holton MAD Scientist Junyu Xiao wrote: Hi all, We run into an interesting space group problem. The same diffraction image can be either indexed into space group C2, with a=145, b=44, c=67, and beta=110.5; or space group P2 (should be P21 after

Re: [ccp4bb] space group problem

Clemens is right of course. If you ignore the lattice centring in C2, the cells are the same. I was however under the impression that auto-indexing goes via the primitive cell. Which makes the two solutions unique. Ignoring the possible lattice translation in P2 will show up in a Patterson

Re: [ccp4bb] space group problem

Dear all, Thanks for all the advices. I am especially grateful to Dr. Clemens Vonrhein, now I am clear about the relationship between this two choices. Dr. Zwart raises another interesting point, which of course is my major concern. C2 will have the advantage for phasing, since it has a

Re: [ccp4bb] space group problem

pseudo C2 centering in P21 will result in C2 systematic absenses being weak. you can check this with e.g. dataman (parity check of even and odd reflections of that type). and you will have that native patterson peak as mentioned. this will make life bit more complicated of course since large