Print

Print
You dont say whether there is Non cryst translation - that will be reported at various stages - the pointless/aimless/ctruncate task gives it.

But if it exists and the translation ihas a component of .5 along any axis, that makes the SG estimate a bit uncertain - the absences could be due to the NX translation.

And even if the SG is correct - which likely after solving the MR with the newest PHASER which tests carefully = then you will have zones with low intensities, and those reflections always have a higher r factor of course. 

You could let Arp/Warp or Buccaneer rebuild starting from your existing model? That is a verification that your solution is essentially right

Eleanor



On 18 March 2017 at 10:28, Isupov, Michail <[log in to unmask]> wrote:
Hi,

I have seen cases where in a correct space group
'R-work and R-free values 0.25 and 0.32 respectively'
at 2 A resolution sound like not too bad values.
In some of such cases when data from a different crystal
in the same space group was available R-factors were much lower
when the structure was refined against the new crystal data.
I guess this phenomenon could be due to uneven freezing of the first crystal,
or inconsistent degree of disorder between crystals.

In other projects high R-factor values (e.g. FreeR around 33% at 2.1 A resolution)
 are consistent through a range of crystals
even when the refinement is in P1, although the map quality is good enough
to see cofactors and to build  the missing parts of the structure (30% of residues).
The disorder seems to be an intrinsic property of such crystal form.

I do not know how to approach publishing these results since most referees will argue
that such R-factors may be acceptable at 4A resolution but not close to 2 Angstrom.

Best wishes,

Misha Isupov
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Randy Read [[log in to unmask]]
Sent: Saturday, March 18, 2017 9:29 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] No improvement in R-factor after Refmac.

Hi,

I was just going to make the same point!  The only thing to add is that, if there really is translational NCS (which is certainly possible with 4 copies in the a.u.), then it’s essential both to account for it (which current versions of Phaser should do automatically, if you search for all 4 copies in one job) and to try all possible space groups.  The situation Craig describes, in which it’s not immediately obvious whether your crystal has a crystallographic 2(1) and a pseudosymmetric non-crystallographic 2-fold or the reverse, is not uncommon.  However, we’ve found that the likelihood score accounting for the effect of tNCS is pretty good at discriminating the two possibilities.

Best wishes,

Randy Read

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

> On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <[log in to unmask]> wrote:
>
> You really need to approach such situations with caution.  Examination of the relatively small number of axial reflections probably show that there might be twofold screw axes in all three directions.  But a non-crystallographic microscopic translation of nearly 0.5 in the direction of a crystallographic axis will give the same pattern of strong and weak reflections as a crystallographic twofold screw axis.  If I were you, I would be very sure to try molecular replacement in all possible orthorhombic space groups.  Several programs, including Phaser, will organize that exhaustive search across all eight possibilities for you.
>
>> On Mar 17, 2017, at 11:56 PM, Polisetty Satya Dev <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> We checked all possible space groups of orthorhombic crystal system using Scala and Pointless but the statistics show that P212121 is the possible space group.
>>
>> Thank You,
>> Satya Dev
>>
>> On Fri, Mar 17, 2017 at 8:03 PM, Teplyakov, Alexey [JRDUS] <[log in to unmask]> wrote:
>> Check the space group. It may be orthorhombic with a pure rotational axis (e.g. P21212) or even monoclinic.
>>
>>
>>
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Polisetty Satya Dev
>> Sent: Friday, March 17, 2017 9:51 AM
>> To: [log in to unmask]
>> Subject: [EXTERNAL] [ccp4bb] No improvement in R-factor after Refmac.
>>
>>
>>
>> Dear all,
>>
>> I solved a structure at 2.0 A resolution with R-work and R-free values 0.25 and 0.32 respectively and I am stuck at Refmac step where there is no further reduction in R-factor.
>>
>> The above stated values were obtained after several rounds of manual refinement followed by refmac. There are also areas where electron density is missing around peptide backbone in one of the monomer in ASU.
>>
>> Can anyone please tell me how can I improve the electron density and R-factor.
>>
>>
>> The structure solution was obtained using Phaser MR and here are the data statistics:
>>
>>
>>
>> Average unit cell: 81.95, 100.40, 156.96,   90.00, 90.00, 90.00,
>> Space group: P212121,
>> Completeness 99.5,
>> Multiplicity 6.4,
>> Four monomers per ASU.
>> Solvent content: 47%.
>>
>> Thank you everyone,
>> Satya Dev,
>> JNCASR.
>>
>