[ccp4bb] Fwd: [ccp4bb] No improvement in R-factor after Refmac.

[Polisetty Satya Dev]

-- Forwarded message --
From: Polisetty Satya Dev <pvss...@gmail.com>
Date: Mon, Mar 20, 2017 at 1:35 PM
Subject: Re: [ccp4bb] No improvement in R-factor after Refmac.
To: Sudipta Bhattacharyya <sudiptabhattacharyya.iit...@gmail.com>


Hi,
I had tried running xtriage but it does not show any sign of NCS. But
pointles is showing the following warning
* "one or more zones have data systematically missing from the input file
thus we cannot determine if reflections are truly systematically absent"*

Thank You,
Satya Dev

On Sun, Mar 19, 2017 at 5:22 AM, Sudipta Bhattacharyya <
sudiptabhattacharyya.iit...@gmail.com> wrote:

> Hi Satya Dev,
>
> You can feed the mtz output of SCALA to Phenix Xtriage and then see the
> presence of t-NCS and/or any other crystal pathologies. Another thing you
> can do is to merge and scale the data in P222 and then let the Phaser
> decide the best space group. Again, I am curious, when you ran pointless,
> did you check the absence conditions and the probability of assigning all
> the three screw axes?
>
> Good luck!
> Sudipta.
>
> On Sat, Mar 18, 2017 at 5:42 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk
> > wrote:
>
>> 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 <m.isu...@exeter.ac.uk> 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy
>>> Read [rj...@cam.ac.uk]
>>> Sent: Saturday, March 18, 2017 9:29 AM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> 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 Cambri

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Sudipta Bhattacharyya]

Hi Satya Dev,

You can feed the mtz output of SCALA to Phenix Xtriage and then see the
presence of t-NCS and/or any other crystal pathologies. Another thing you
can do is to merge and scale the data in P222 and then let the Phaser
decide the best space group. Again, I am curious, when you ran pointless,
did you check the absence conditions and the probability of assigning all
the three screw axes?

Good luck!
Sudipta.

On Sat, Mar 18, 2017 at 5:42 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk>
wrote:

> 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 <m.isu...@exeter.ac.uk> 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy
>> Read [rj...@cam.ac.uk]
>> Sent: Saturday, March 18, 2017 9:29 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> 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 ResearchTel: +44 1223 336500
>> Wellcome Trust/MRC Building Fax: +44 1223 336827
>> Hills Road
>> E-mail: rj...@cam.ac.uk
>> Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>
>> > On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <cabing...@wisc.edu> 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 th

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Eleanor Dodson]

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 <m.isu...@exeter.ac.uk> 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read
> [rj...@cam.ac.uk]
> Sent: Saturday, March 18, 2017 9:29 AM
> To: CCP4BB@JISCMAIL.AC.UK
> 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 ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <cabing...@wisc.edu> 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 <pvss...@gmail.com>
> 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] <
> atepl...@its.jnj.com> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Polisetty Satya Dev
> >> Sent:

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Isupov, Michail]

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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read 
[rj...@cam.ac.uk]
Sent: Saturday, March 18, 2017 9:29 AM
To: CCP4BB@JISCMAIL.AC.UK
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 ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <cabing...@wisc.edu> 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 <pvss...@gmail.com> 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] 
>> <atepl...@its.jnj.com> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Polisetty Satya Dev
>> Sent: Friday, March 17, 2017 9:51 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> 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.
>>
>

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Randy Read]

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 ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 18 Mar 2017, at 06:12, CRAIG A BINGMAN <cabing...@wisc.edu> 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 <pvss...@gmail.com> 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] 
>> <atepl...@its.jnj.com> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Polisetty Satya Dev
>> Sent: Friday, March 17, 2017 9:51 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> 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.
>> 
> 

Re: [ccp4bb] No improvement in R-factor after Refmac.

[CRAIG A BINGMAN]

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 
<pvss...@gmail.com<mailto:pvss...@gmail.com>> 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] 
<atepl...@its.jnj.com<mailto:atepl...@its.jnj.com>> 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:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of 
Polisetty Satya Dev
Sent: Friday, March 17, 2017 9:51 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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.

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Polisetty Satya Dev]

Hi,

We ran Scala program with 2 A resolution cut-off and it gave mean I / sig I
value as follows

Overall: 7.3   OuterShell: 2.0 InnerShell: 16.5

CC(1/2) : Overall: 0.994   OuterShell: 0.665 InnerShell: 0.997

We also tried Scala with 2.33 A resolution cut-off and the statistics are
as follows

Mean I / sig I : Overall: 11.3   OuterShell: 5.0 InnerShell: 20.0

CC(1/2) : Overall: 0.995   OuterShell: 0.942 InnerShell: 0.997

Thank You,
Satya Dev.

On Fri, Mar 17, 2017 at 7:59 PM, Mohamed Noor  wrote:

> How do you know it's really 2 A resolution? How is your CC(1/2)?
>
>
> On 17/03/2017 13:51, Polisetty Satya Dev wrote:
>
> 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.
>
>
>

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Polisetty Satya Dev]

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] <
atepl...@its.jnj.com> 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:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Polisetty
> Satya Dev
> *Sent:* Friday, March 17, 2017 9:51 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *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.
>

Re: [ccp4bb] No improvement in R-factor after Refmac.

[Masooma Rasheed]

One way is to refine the best chain out of four, first and then generate a
seperate pdb for that chain only and use molecular replacement to find the
rest of the three chains. It does help with improving map to certain
extent. Also delete the missing residues one by one and then run refmac to
see if get any green density back for them to rebuild them in the right
conformation..

On Fri, Mar 17, 2017 at 1:51 PM, Polisetty Satya Dev 
wrote:

> 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.
>
>


-- 
Dr. Masooma Rasheed
Division of Molecular Biosciences
Biochemistry Building Level 5
Imperial College London
South Kensington
London SW7 2AZ
UK

[ccp4bb] No improvement in R-factor after Refmac.

[Polisetty Satya Dev]

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.