Hello,

I would like to ask a question related to a recent thread regarding
bad/missing density.

I have used SAD to solve the structure of a protein at about 2.6Å
resolution. Phenix build a good portion of it (about 50%) and the density
in this region is good. However, we cannot see ther rest 50%.  Rfree is
currently at 32%.  No twinning is suggested.

How can we "find" the missing 50%? We have tried MR-SAD with no significant
improvement. We know the missing mass is there because we ran the crystals
on a  gel, and the protein is intact.

I know with MR sometimes the space group can make a difference, but with
experimental phasing (SAD),  if the space group were incorrectly
identified, would we have gotten a solution to the Se substructure? This
seems correct because the visible 50% of the protein make total sense. So,
since we have a correct substructure, can I conclude with confidence that
the space group is correctly identified?

Of course, it could be that the missing bit is very flexible and does not
scatter coherently, but then, wouldn't we expect a lower Rfree?

Thanks so much!

Claire






On Wed, Jan 25, 2017 at 7:00 PM, CCP4BB automatic digest system <
lists...@jiscmail.ac.uk> wrote:

> There are 13 messages totaling 4586 lines in this issue.
>
> Topics of the day:
>
>   1. add ligand solution onto drop directly (2)
>   2. Bad density for chains (3)
>   3. Unknown electron density blob (2)
>   4. Macromolecular Crystallography School MCS2017 Madrid
>   5. explain "comfortable"
>   6. Unknown electron density blob, pdb convention for partially ordered
>      ligands (3)
>   7. PhD Presidential fellowship to study the Structure and function of
> CRISPR
>      systems
>
> ----------------------------------------------------------------------
>
> Date:    Wed, 25 Jan 2017 03:23:18 +0100
> From:    Markus Heckmann <markus.21...@gmail.com>
> Subject: add ligand solution onto drop directly
>
> Dear all,
> I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the
> drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of
> dissolving it in precipitant solution and transferring the crystal to this
> ligand containing precipitant solution. The crystals survive this as I add
> the ligand solution to the edge of the drop and gently mix the two
> solutions. Since I collected my datasets I wonder if it is OK?
>
> Many thanks,
> Markus
>
> ------------------------------
>
> Date:    Tue, 24 Jan 2017 19:15:43 -0800
> From:    Bernhard Rupp <hofkristall...@gmail.com>
> Subject: Re: add ligand solution onto drop directly
>
> The truth is in the map. Ergo, zap it and rationalize why it worked or not
> later.
>
>
>
> Cheers, BR
>
>
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Markus Heckmann
> Sent: Tuesday, January 24, 2017 6:23 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] add ligand solution onto drop directly
>
>
>
> Dear all,
>
> I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the
> drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of
> dissolving it in precipitant solution and transferring the crystal to this
> ligand containing precipitant solution. The crystals survive this as I add
> the ligand solution to the edge of the drop and gently mix the two
> solutions. Since I collected my datasets I wonder if it is OK?
>
> Many thanks,
>
> Markus
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 10:12:55 +0530
> From:    Pooja Kesari <pkesar...@gmail.com>
> Subject: Bad density for chains
>
> Dear All,
>
> I have a 2.6 A resolution structure having four chains in an asymmetric
> unit.
> The chain A and B have density for almost all residues however we don't
> have proper residue density in chain C and D.What can be tried to build
> chain C and D ?
>
>
>
> Many Thanks
> Pooja
>
> ------------------------------
>
> Date:    Tue, 24 Jan 2017 21:02:40 -0800
> From:    Debanu <debanu....@gmail.com>
> Subject: Re: Bad density for chains
>
> Hi Pooja,
>
> Are you positive you have the correct space group and there are no other
> issues like twinning, etc?
>
> If sure, did you define NCS groups in refinement? TLS refinement? Try
> different refinement programs?
>
> How big is the molecule? Was it solved by MR or experimental phasing?
>
> You can try superimposing A/B on C/D and refinement with tight NCS then
> adjust NCS restraints during model adjustments based on local differences
> or also see if phenix autobuild helps.
>
> Best,
> Debanu
> --
> Debanu Das
> Accelero Biostructures
>
>
> > On Jan 24, 2017, at 8:42 PM, Pooja Kesari <pkesar...@gmail.com> wrote:
> >
> > Dear All,
> >
> > I have a 2.6 A resolution structure having four chains in an asymmetric
> unit.
> > The chain A and B have density for almost all residues however we don't
> have proper residue density in chain C and D.What can be tried to build
> chain C and D ?
> >
> >
> >
> > Many Thanks
> > Pooja
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 05:11:56 +0000
> From:    Robbie Joosten <robbie_joos...@hotmail.com>
> Subject: Re: Unknown electron density blob
>
> PEG likes to hang around where it is unwelcome:
> http://onlinelibrary.wiley.com/doi/10.1002/pro.2923/full
>
> Cheers,
> Robbie
>
> Sent from my Windows 10 phone
>
> Van: Bernhard Rupp<mailto:hofkristall...@gmail.com>
> Verzonden: dinsdag 24 januari 2017 23:20
> Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Onderwerp: Re: [ccp4bb] Unknown electron density blob
>
> Some general remarks about PEG modelling and associated caveats:
> http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html
> Section 3.6.5.
>
> Best, BR
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ana
> Luísa Moreira de Carvalho
> Sent: Tuesday, January 24, 2017 10:11 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Unknown electron density blob
>
> Just to add to this, in our group, we had a funny case where we found PEG
> around K:
>
> https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
> https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc
>
> Ana Luisa
>
>
> On 24 Jan 2017, at 17:36, Artem Evdokimov <artem.evdoki...@gmail.com<
> mailto:artem.evdoki...@gmail.com>> wrote:
>
> PEG. It wraps around K or R residues just like you are showing.
>
> Artem
> www.harkerbio.com<http://www.harkerbio.com/>
> "where every blob has candy inside"
>
> On Jan 24, 2017 12:19 PM, "Uma Gabale" <00000ebb5dcf3eaa-dmarc-
> requ...@jiscmail.ac.uk<mailto:00000ebb5dcf3eaa-dmarc-
> requ...@jiscmail.ac.uk>> wrote:
> Dear all,
> While refining a structure at 2.5 A resolution, we observed a
> semi-circular/crescent shaped electron density blob as shown in the
> attached picture. We have been unable to identify it so far, and would
> appreciate any help in identification.
> The protein was expressed in E. coli BL21(DE3), purified on Ni-NTA
> followed by gel filtration. The purification buffers included Tris and NaCl
> (no detergent/ other ingredients except for imidazole for Ni-NTA).
> Crystallization condition had HEPES and PEG3350; no cryoprotectant was used.
> The blob is surrounded by residues Trp, Thr, Gln, Arg, and Phe.
> Thanks and regards,
> Uma.
>
> --
> Uma Gabale, PhD
> Research Associate
> Molecular and Cellular Biochemistry
> Indiana University Bloomington
>
> Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
> ************************************************************
> ***************
> Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
> Dep. Quimica, FCT-UNL
> 2829-516 Caparica
> Portugal
> Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
> Fax: 00351212948550
> http://docentes.fct.unl.pt/almc
> http://sites.fct.unl.pt/xtal
> https://www.facebook.com/XtalNOVA/
> ************************************************************
> ***************
> Single Crystal X-ray Structure Determination Service:
> http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 11:05:22 +0100
> From:    Juan Antonio Hermoso <xj...@iqfr.csic.es>
> Subject: Macromolecular Crystallography School MCS2017 Madrid
>
> Dear colleagues,
>
>
>
> We are pleased to announce the eighth edition of the Macromolecular
> Crystallography School 2017, to
>
> be held at the Institute Química-Física Rocasolano- CSIC (Madrid, Spain).
>
> Dates: May 5 - 10, 2017
>
> Invited speakers and tutors:
>
> - Paul Adams, Berkeley, USA
>
> - Pavel Afonine, Berkeley, USA
>
> - Armando Albert, Madrid, Spain
>
> - Roeland Boer, Barcelona, Spain
>
> - Jose M Carazo, Madrid, Spain
>
> - Kay Diederichs, Konstanz, Germany
>
> - Paul Emsley, Cambridge, UK
>
> - Rafael Fernández-Leiro, Cambridge, UK
>
> - Carmelo Giacovazzo, Bari, Italy
>
> - Xavier Gomis-Ruth, Barcelona, Spain
>
> - Juan A. Hermoso, Madrid, Spain
>
> - Eugene Krissinel, Oxford, UK
>
> - José Martín-García, Arizona, USA
>
> - Rob Nicholls, Cambridge, UK
>
> - Maria Solá, Barcelona, Spain
>
> - Isabel Usón, Barcelona, Spain
>
>
>
> Please find attached the program of the Workshop, the application form
> and  further information, at http://www.xtal.iqfr.csic.es/MCS2017/ <
> http://www.xtal.iqfr.csic.es/MCS2017/>
>
>
> Applicants:
>
> The workshop has been designed for postgraduate, postdoctoral and
> research scientists that deal with macromolecular crystallography but
>
> need further knowledge on the routine uses, the state of the art and
> fundamentals that underlie the modern techniques for macromolecular
>
> crystallography. The topics will cover crystallographic computing and
> fundamentals using XDS, CCP4 and Phenix, as well as the state of the
>
> art on topics such as the strategies for protein production, data
> collection,phasing and refinement with ARCCIMBOLDO, SHELX and SIR2014 and
> modeling
>
> with COOT.
>
> This year we have introduced full-day on breakthrough techniques such as
> XFEL and cryo EM.
>
>
>
> MCS2017 will provide six days of lectures and  workshops. The course is
> designed for 25 highly motivated attendants.
>
>
>
> Requests to participate must be sent by a free-formated E-mail, before
> March 10, 2017 to the following address: cur...@fgua.es <mailto:
> cur...@fgua.es>, indicating
>
> the motivation to participate and experience on macromolecular
> crystallography and including a letter of recommendation from PhD
>
> Director (only for PhD students).
>
> Accepted participants will be notified by e-mail before March 17, 2017.
>
> Organizers:
>
> Armando Albert (xalb...@iqfr.csic.es <mailto:xalb...@iqfr.csic.es> ),
> Juan A. Hermoso
>
> (xj...@iqfr.csic.es <mailto:xj...@iqfr.csic.es>) and Isabel Usón (
> iuf...@ibmb.csic.es <mailto:iuf...@ibmb.csic.es>)
>
>
>
> ___________________________________
>
> Prof. Dr. Juan A. Hermoso
> Dept. Crystallography & Structural Biology.
> Inst. Quimica-Fisica "Rocasolano". CSIC (Spanish National Research Council)
> Serrano 119. 28006-Madrid.
> Spain
> Phone: +34 917459538
> Fax: +34 915642431
> E-mail: xj...@iqfr.csic.es
> Web site: http://www.xtal.iqfr.csic.es/grupo/xjuan/
> ___________________________________
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 14:51:20 +0000
> From:    Uma Gabale <umaka...@yahoo.com>
> Subject: Re: Unknown electron density blob
>
> Dear all,Thank you very much for your replies. It is a PEG, a "di"ethylene
> glycol to be precise, in most chains. Best regards,Uma. --Uma Gabale,
> PhDResearch AssociateMolecular and Cellular Biochemistry
> Indiana University Bloomington
>
> #yiv6125321912 #yiv6125321912 -- _filtered #yiv6125321912
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> .yiv6125321912MsoChpDefault {} _filtered #yiv6125321912 {margin:70.85pt
> 70.85pt 70.85pt 70.85pt;}#yi
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 08:05:40 -0800
> From:    Bernhard Rupp <hofkristall...@gmail.com>
> Subject: explain "comfortable"
>
> Hi Fellows,
>
>
>
> JPK has made a valid point by reminding me that my "statement about
> becoming
> "comfortable" with a particular level of conservatism/enthusiasm"
>
> made in the N14 paper seems like a very non-scientific standard.
>
>
>
> He is right. Let me explain: The difference between enthusiastic modelling
> and being a reckless over-modeller is dependent on your objective, that is,
> what
>
> hypothesis or claims is your model at that specific location supposed to
> support? This is a question that no statistic or metric is going to answer
> for you.
>
> There is indeed room for interpretation - after all it is *electron density
> interpretation* what we do, and some are more perceptive than others; such
>
> is the artistic (or artisan) and perhaps enjoyable part in model building.
> As long as the postulate is plausible, you do have a certain degree of
> reasonable freedom.
>
> Solvent for example, is fluid and floating, after all. But also solvent
> modeling does have some rules, consequences and meaning.
>
>
>
> It is important not mistake this disclaimer for a postmodern argument
> justifying 'Anything goes'. If one's claim is to support a certain
> mechanistic detail or
>
> ligand pose, one better cough up some convincing, properly generated and
> adequately contoured difference electron density and a model that is not
> delusional in
>
> view of basic stereochemistry.
>
> Sorry for being redundant.
>
>
>
> Best, BR
>
> ------------------------------------------------------
>
> Bernhard Rupp
>
>  <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/
>
>  <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 767 571 0536
>
> ------------------------------------------------------
>
> All models are wrong
>
> but some are useful.
>
> ------------------------------------------------------
>
>
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 16:09:42 +0000
> From:    "Phoebe A. Rice" <pr...@uchicago.edu>
> Subject: Re: Bad density for chains
>
> Are you sure there really are 4 chains?  50% solvent may be average, but
> we've had crystals with closer to 80%.
>
>
> ________________________________
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Pooja
> Kesari [pkesar...@gmail.com]
> Sent: Tuesday, January 24, 2017 10:42 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Bad density for chains
>
> Dear All,
>
> I have a 2.6 A resolution structure having four chains in an asymmetric
> unit.
> The chain A and B have density for almost all residues however we don't
> have proper residue density in chain C and D.What can be tried to build
> chain C and D ?
>
>
>
> Many Thanks
> Pooja
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 12:21:03 -0500
> From:    "Edward A. Berry" <ber...@upstate.edu>
> Subject: Re: Unknown electron density blob, pdb convention for partially
> ordered ligands
>
> Uma's use of quotes around "di" suggests a related question about PDB
> convention. It was my (perhaps not very good) understanding that ligands
> should be identified by what is actually present in the crystal, and not by
> what can be modeled. For example endogenous ubiquinone is likely to be UQ50
> (depending on the species) but most of that 50-carbon side chain is hanging
> out in the lipid or detergent and completely disordered. Still we should
> use the ligand identifier for UQ50, even though codes exist for UQ with 5
> or 10-carbon side chains that are much better accommodated by the density.
>
> If that is the case, one should not use the pdb identifier for diethylene
> glycol (PEG) when PEG4k was the precipitant, unless you believe that the
> binding site has specifically selected diethylene glycol from an extremely
> broad range of polymer lengths in the added material.  Using the identifier
> for a much longer PEG will result in a large number of "missing atoms"
> listed in the report, but would eliminate the unreasonable assumption that
> PEG fragment models must always end with a terminal oxygen.
>
> Even if that is the rule, I would agree that PEGs would be a good place to
> ignore the rule. Since PEGs have a MW distribution, it is impossible to
> know exactly what is bound and it may be different in different unit cells.
> If you are not going to get it right no matter what you put, you might as
> well put something that fits.
> eab
>
> On 01/25/2017 09:51 AM, Uma Gabale wrote:
> > Dear all,
> > Thank you very much for your replies. It is a PEG, a "di"ethylene glycol
> to be precise, in most chains.
> > Best regards,
> > Uma.
> > --
> > Uma Gabale, PhD
> > Research Associate
> > Molecular and Cellular Biochemistry
> > Indiana University Bloomington
> >
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 17:29:36 +0000
> From:    Tristan Croll <ti...@cam.ac.uk>
> Subject: Re: Unknown electron density blob, pdb convention for partially
> ordered ligands
>
> I've often wondered about PEG (and, I guess, other synthetic polymers):
> wouldn't it just be better to define the monomer, and then model a chain of
> however many monomers you need?
>
> T
>
>
>
> Tristan Croll
> Research Fellow
> Cambridge Institute for Medical Research
> University of Cambridge CB2 0XY
>
>
>
>
> > On 25 Jan 2017, at 17:21, Edward A. Berry <ber...@upstate.edu> wrote:
> >
> > Uma's use of quotes around "di" suggests a related question about PDB
> convention. It was my (perhaps not very good) understanding that ligands
> should be identified by what is actually present in the crystal, and not by
> what can be modeled. For example endogenous ubiquinone is likely to be UQ50
> (depending on the species) but most of that 50-carbon side chain is hanging
> out in the lipid or detergent and completely disordered. Still we should
> use the ligand identifier for UQ50, even though codes exist for UQ with 5
> or 10-carbon side chains that are much better accommodated by the density.
> >
> > If that is the case, one should not use the pdb identifier for
> diethylene glycol (PEG) when PEG4k was the precipitant, unless you believe
> that the binding site has specifically selected diethylene glycol from an
> extremely broad range of polymer lengths in the added material.  Using the
> identifier for a much longer PEG will result in a large number of "missing
> atoms" listed in the report, but would eliminate the unreasonable
> assumption that PEG fragment models must always end with a terminal oxygen.
> >
> > Even if that is the rule, I would agree that PEGs would be a good place
> to ignore the rule. Since PEGs have a MW distribution, it is impossible to
> know exactly what is bound and it may be different in different unit cells.
> If you are not going to get it right no matter what you put, you might as
> well put something that fits.
> > eab
> >
> >> On 01/25/2017 09:51 AM, Uma Gabale wrote:
> >> Dear all,
> >> Thank you very much for your replies. It is a PEG, a "di"ethylene
> glycol to be precise, in most chains.
> >> Best regards,
> >> Uma.
> >> --
> >> Uma Gabale, PhD
> >> Research Associate
> >> Molecular and Cellular Biochemistry
> >> Indiana University Bloomington
> >>
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 10:27:26 -0700
> From:    Ryan Jackson <ryja...@gmail.com>
> Subject: PhD Presidential fellowship to study the Structure and function
> of CRISPR systems
>
> The Jackson Lab (http://www.chem.usu.edu/people/faculty/ryan-jackson) at
> Utah State University seeks a qualified graduate for a 2017 Presidential
> Doctoral Research Fellow position (http://rgs.usu.edu/pdrf/) with a living
> stipend of $30,000 to study the structure and function of newly discovered
> CRISPR immune systems.  The fellow will use protein crystallography,
> cryo-electron microscopy, biochemical and biophysical techniques to study
> CRISPR system structure and function.
>
> Basic requirements for the position are a GPA of 3.5 or higher and a GRE
> score above the 70th percentile.
>
> Please email applications to ryan.jack...@usu.edu
>
> The application should include a curriculum vitae with a description of
> past research experience and accomplishments, a current academic
> transcript, GRE scores, and three letters of reference.
>
> If there any questions about the application requirement please email
> ryan.jack...@usu.edu.
>
>
> --
> Ryan N Jackson, PhD
> Assistant Professor
> Dept. Chemistry and Biochemistry
> Utah State University
> Logan UT, 84322
> phone: 435-797-1635
> fax:435-797-3390
>
> ------------------------------
>
> Date:    Wed, 25 Jan 2017 18:09:44 +0000
> From:    Robbie Joosten <robbie_joos...@hotmail.com>
> Subject: Re: Unknown electron density blob, pdb convention for partially
> ordered ligands
>
> Hi Tristan,
>
>
>
> There are PDB entries that have this, but this makes matters a bit more
> complicated in annotation. You have to define LINKs and leaving atoms.
> Consistency would be nice here, but that is lacking in these entries.
>
>
>
> Cheers,
>
> Robbie
>
>
>
> Sent from my Windows 10 phone
>
>
>
> Van: Tristan Croll<mailto:ti...@cam.ac.uk>
> Verzonden: woensdag 25 januari 2017 18:30
> Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Onderwerp: Re: [ccp4bb] Unknown electron density blob, pdb convention for
> partially ordered ligands
>
>
>
> I've often wondered about PEG (and, I guess, other synthetic polymers):
> wouldn't it just be better to define the monomer, and then model a chain of
> however many monomers you need?
>
> T
>
>
>
> Tristan Croll
> Research Fellow
> Cambridge Institute for Medical Research
> University of Cambridge CB2 0XY
>
>
>
>
> > On 25 Jan 2017, at 17:21, Edward A. Berry <ber...@upstate.edu> wrote:
> >
> > Uma's use of quotes around "di" suggests a related question about PDB
> convention. It was my (perhaps not very good) understanding that ligands
> should be identified by what is actually present in the crystal, and not by
> what can be modeled. For example endogenous ubiquinone is likely to be UQ50
> (depending on the species) but most of that 50-carbon side chain is hanging
> out in the lipid or detergent and completely disordered. Still we should
> use the ligand identifier for UQ50, even though codes exist for UQ with 5
> or 10-carbon side chains that are much better accommodated by the density.
> >
> > If that is the case, one should not use the pdb identifier for
> diethylene glycol (PEG) when PEG4k was the precipitant, unless you believe
> that the binding site has specifically selected diethylene glycol from an
> extremely broad range of polymer lengths in the added material.  Using the
> identifier for a much longer PEG will result in a large number of "missing
> atoms" listed in the report, but would eliminate the unreasonable
> assumption that PEG fragment models must always end with a terminal oxygen.
> >
> > Even if that is the rule, I would agree that PEGs would be a good place
> to ignore the rule. Since PEGs have a MW distribution, it is impossible to
> know exactly what is bound and it may be different in different unit cells.
> If you are not going to get it right no matter what you put, you might as
> well put something that fits.
> > eab
> >
> >> On 01/25/2017 09:51 AM, Uma Gabale wrote:
> >> Dear all,
> >> Thank you very much for your replies. It is a PEG, a "di"ethylene
> glycol to be precise, in most chains.
> >> Best regards,
> >> Uma.
> >> --
> >> Uma Gabale, PhD
> >> Research Associate
> >> Molecular and Cellular Biochemistry
> >> Indiana University Bloomington
> >>
>
> ------------------------------
>
> End of CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)
> ************************************************************
>

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