Re: [ccp4bb] add ligand with AceDRG
Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria > On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE > wrote: > > Hi all, > > I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: > > I put in a smilesstring and the ligand is written ok, but since I can only > chose already 'taken' 3-letter-codes the refinement always crashes as there > is a clash with existing library entries. > Is there any way around this? How do I add a novel ligand? > > Thanks so much for your help. > > Best wishes, > Stefanie > > > > Dr. Stefanie Freitag-Pohl (she/her) > Durham University > Department of Chemistry > South Road, Durham > DH1 3LE > United Kingdom > 0191 334 2596 > stefanie.freitag-p...@durham.ac.uk <mailto:stefanie.freitag-p...@durham.ac.uk> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 Maria Håkansson, PhD, Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] disordered cysteine
Dear Oliviero, Resending the message since I am not sure you got it. For sure cysteines can be disordered. Sometimes you can find one conformation reduced and another conformation oxidised if the cysteine is solvent exposed. Also in well-resolved structures you can see a cysteine taking part in a disulphide bond, but only partially, one conformation being unbound. This can have to do with how you treated your protein with reducing agents but probably also depend on how easily reduced the disulphide bond is. Also cysteines can be modified by beta-mercaptoethanol if this chemical is added in large amounts and the cysteines are solvent exposed. More seldom I have seen double conformation alone of cysteines but I guess this may occur as well. It can be difficult to correctly model oxidised and reduced or native cysteines in the same residue since the residue names differ (and you can only have one name). Depending on occupancy I usually use CYS only if lower occupancy of the oxidised form or if higher occupancy of the oxidised form CSO for both (could be other species too), possibly with zero occupancy on the oxygen missing. Maybe there is better suggestions? Sorry not to be able to share any references. Good luck! Best regards, Maria > On 22 Apr 2024, at 10:55, Italo Carugo Oliviero > wrote: > > Dears, > is it possible for a cysteine to be conformationally disordered? It seems > strange to me. If it were, it would almost certainly be exposed to the > solvent and thus easily oxidized irreversibly. Do you perhaps have any > information on conformationally disordered cysteines? > I thank you, > Oliviero > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > Maria Håkansson, PhD, Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] disordered cysteine
Dear Oliviero, For sure cysteines can be disordered. Sometimes you can find one conformation reduced and another conformation oxidised if the cysteine is solvent exposed. Also in well-resolved structures you can see a cysteine taking part in a disulphide bond, but only partially, one conformation being unbound. This can have to do with how you treated your protein with reducing agents but probably also depend on how easily reduced the disulphide bond is. Also cysteines can be modified by beta-mercaptoethanol if this chemical is added in large amounts and the cysteines are solvent exposed. More seldom I have seen double conformation alone of cysteines but I guess this may occur as well. It can be difficult to correctly model oxidised and reduced or native cysteines in the same residue since the residue names differ (and you can only have one name). Depending on occupancy I usually use CYS only if lower occupancy of the oxidised form or if higher occupancy of the oxidised form CSO for both (could be other species too), possibly with zero occupancy on the oxygen missing. Maybe there is better suggestions? Sorry not to be able to share any references. Good luck! Best regards, Maria > On 22 Apr 2024, at 10:55, Italo Carugo Oliviero > wrote: > > Dears, > is it possible for a cysteine to be conformationally disordered? It seems > strange to me. If it were, it would almost certainly be exposed to the > solvent and thus easily oxidized irreversibly. Do you perhaps have any > information on conformationally disordered cysteines? > I thank you, > Oliviero > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > Maria Håkansson, PhD, Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Extra density close to phosphate bound to Zn2+
Hi, Thanks for your suggestions but I have tried to invert the phosphate and it is not fitting the map. The geometry is not correct that way and it is too good data to ignore and to my knowledge a pentacoordinated phosphate is a non existent species. That leaves me with ions. Best regards, Maria Maria Håkansson, PhD, Crystallization Facility Manager Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com > On 5 Aug 2019, at 16:32, Jan Abendroth wrote: > > Hi Maria, > apart from the suggestions that were already made, take a look at the P-O > bond on the right side of the P. Maybe it is just the perspective, this > appears to be rather long. > So, instead of the alternate conformation, maybe just a flip of the phosphate > and a water off to the right? > > Cheers, > Jan > > On Mon, Aug 5, 2019 at 7:16 AM Nukri Sanishvili <mailto:sannu...@gmail.com>> wrote: > Hi Maria, > Let's not ignore the "missing" density - the red one. If the question is only > P vs S, a sulfur would add to the negative density, i.e. make matters worse. > It also appears that modeling a phosphate in alternative conformations, as > suggested by Wim and Roger, would take care of the issue of negative density > as well. > Cheers, > Nukri > > On Mon, Aug 5, 2019 at 8:05 AM Maria Håkansson <mailto:maria.hakans...@saromics.com>> wrote: > Dear CCP4 bulletin board, > > I am working with some lytic enzymes called endolysines, which > bind Zn2+ in the active site. I have three homologues protein > determined to 1.2 Å each where the Zn2+ is bound > to a cystein, two histidines and one phosphate ion added (1.9-2.3 Å binding > distances) in the crystallization experiment. > > Now to my question. Close to the phosphate (B-factor=20Å2) ion a 8 sigma peak > is present in all three endolysines, see below. > I have modeled it to a Na+ (B-factor= 30 Å2) or a Li+ (B factor = 13Å2) ion. > Sodium has benn added in the crystallization experiments since sodium > potassium phosphate > salt has been used. The only reason for including Li+ is that I think the > binding distances (1.7-2.0 Å) are too short for Na+. > > I have also tried to make a model with the phosphate in two different > conformations but it does not fit. > > Have anyone seen something similar before? What is the most correct way of > dealing with unknown densities? > It is difficult to disregard +8 sigma difference density close to the active > site. > > Thanks in advance for any help! > > Best regards, > Maria > > ion.png> > > Maria Håkansson, PhD, Crystallization Facility Manager > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 > Web: www.saromics.com <http://www.saromics.com/> > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > > -- > Jan Abendroth > Emerald Biostructures > Seattle / Bainbridge Island, WA, USA > home: Jan.Abendroth_at_gmail.com <http://jan.abendroth_at_gmail.com/> > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com <http://www.emeraldbiostructures.com/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Automatic restraints in Refmac too loose?
Hi Garib, Any news? Best regards, Maria Maria Håkansson, PhD, Crystallization Facility Manager Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com > On 29 Jan 2018, at 19:06, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> wrote: > > Yes, it should be as simple as this. But first let me test and see what is > the problem. > > Regards > Garib > > > On 29 Jan 2018, at 17:48, Maria Håkansson <maria.hakans...@saromics.com > <mailto:maria.hakans...@saromics.com>> wrote: > >> Hi Garib, >> >> Usually I update from ccp4. >> >> But I guess if it just to replace the refmac file in the bin directory under >> ccp4-7.0 >> I think I can manage. Is it so? >> >> Best, >> Maria >> >> Maria Håkansson, PhD, Crystallization Facility Manager >> Principal Scientist >> >> SARomics Biostructures AB >> Medicon Village >> SE-223 81 Lund, Sweden >> >> Mobile: +46 (0)76 8585706 >> Web: www.saromics.com <http://www.saromics.com/> >> >> >> >> >>> On 29 Jan 2018, at 18:43, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk >>> <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: >>> >>> Thank you. >>> Do you usually update from ccp4 or you can copy binary file if I send you? >>> >>> Regards >>> Garib >>> >>> >>> On 29 Jan 2018, at 17:42, Maria Håkansson <maria.hakans...@saromics.com >>> <mailto:maria.hakans...@saromics.com>> wrote: >>> >>>> Hi Garib, >>>> >>>> It says: Refmac version 5.8.0189 : 21/09/17 >>>> >>>> Best regards, >>>> Maria >>>> >>>> Maria Håkansson, PhD, Crystallization Facility Manager >>>> Principal Scientist >>>> >>>> SARomics Biostructures AB >>>> Medicon Village >>>> SE-223 81 Lund, Sweden >>>> >>>> Mobile: +46 (0)76 8585706 >>>> Web: www.saromics.com <http://www.saromics.com/> >>>> >>>> >>>> >>>> >>>>> On 29 Jan 2018, at 18:40, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk >>>>> <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: >>>>> >>>>> Hi Maria, >>>>> >>>>> What is the refmac version? It should be on the top of the log file. >>>>> >>>>> Regards >>>>> Garib >>>>> >>>>> >>>>> On 29 Jan 2018, at 17:03, Maria Håkansson <maria.hakans...@saromics.com >>>>> <mailto:maria.hakans...@saromics.com>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I have a question regarding the automatic restraints in Refmac5 and >>>>>> CCP4Interface 7.0.050. >>>>>> >>>>>> For a few years I have relied on automatic restraints settings in the >>>>>> CCP4I interface which >>>>>> usually resulted in r.m.s. bond deviations of about 0.02 Å and good >>>>>> convergence of refinement (lower >>>>>> R-factors). The last few months this have not been the >>>>>> case. In structure after structure in different projects we get >>>>>> consistently r.m.s. deviations of 0.03 Å and more >>>>>> and lacking or worse convergence. This is not a huge problem since you >>>>>> can get around it by using user >>>>>> set weighting terms. Still it is annoying. >>>>>> >>>>>> Anyone experiencing the same? >>>>>> >>>>>> Best regards, >>>>>> Maria >>>>>> >>>>>> >>>>>> Maria Håkansson, PhD, Crystallization Facility Manager >>>>>> Principal Scientist >>>>>> >>>>>> SARomics Biostructures AB >>>>>> Medicon Village >>>>>> SE-223 81 Lund, Sweden >>>>>> >>>>>> Mobile: +46 (0)76 8585706 >>>>>> Web: www.saromics.com <http://www.saromics.com/> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> Dr Garib N Murshudov >>>>> MRC-LMB >>>>> Francis Crick Avenue >>>>> Cambridge >>>>> CB2 0QH UK >>>>> Web http://www.mrc-lmb.cam.ac.uk <http://www.mrc-lmb.cam.ac.uk/>, >>>>> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ >>>>> <http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/> >>>>> >>>>> >>>>> >>>> >>> >>> Dr Garib N Murshudov >>> MRC-LMB >>> Francis Crick Avenue >>> Cambridge >>> CB2 0QH UK >>> Web http://www.mrc-lmb.cam.ac.uk <http://www.mrc-lmb.cam.ac.uk/>, >>> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ >>> <http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/> >>> >>> >>> >> > > Dr Garib N Murshudov > MRC-LMB > Francis Crick Avenue > Cambridge > CB2 0QH UK > Web http://www.mrc-lmb.cam.ac.uk <http://www.mrc-lmb.cam.ac.uk/>, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > <http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/> > > >
[ccp4bb] Automatic restraints in Refmac too loose?
Hi, I have a question regarding the automatic restraints in Refmac5 and CCP4Interface 7.0.050. For a few years I have relied on automatic restraints settings in the CCP4I interface which usually resulted in r.m.s. bond deviations of about 0.02 Å and good convergence of refinement (lower R-factors). The last few months this have not been the case. In structure after structure in different projects we get consistently r.m.s. deviations of 0.03 Å and more and lacking or worse convergence. This is not a huge problem since you can get around it by using user set weighting terms. Still it is annoying. Anyone experiencing the same? Best regards, Maria Maria Håkansson, PhD, Crystallization Facility Manager Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com
[ccp4bb] Micromatrix seeding using the mosquito
Dear all, Anyone who have had success using the mosquito for micromatrix seeding? Which way is the optimal way of adding seed solution to sitting drops on an MRC plate? Is it better to add 100 nl protein + 10 nl seed solution + 100 nl reservoir solution or to add concentrated seed solution (1 microliter) directly to the reservoir solution and then pipett 100 nl protein + 100 nl reservoir solution. Best regards and thanks in advance, Maria Håkansson __ Maria Håkansson, Ph.D. Senior Scientist, Max-lab, Lund University Phone: +46 (0) 76 8585 706 Fax: +46 (0) 46 222 47 10 Ole Römers väg 1 (P.O. Box 188) SE-221 00 Lund, Sweden Web address: www.maxlab.lu.se Email: maria.hakans...@maxlab.lu.se __
[ccp4bb] Stabilization of sensitive crystals - use of glutaraldehyde
Dear All, I have a question about the use of glutaraldehyde as a cross-linking agent. It is a practical question. The glutaraldehyde you can buy from Sigma- Aldrich contains a mixture of polymers according to the product information with an increasing number of polymers with increasing pH. Is it this mixture that is used for cross-linking crystals or do crystallographers use monomeric glutaraldehyde purified on charcoal? Best regards, Maria Håkansson __ Maria Håkansson, Ph.D. Senior Scientist, Max-lab, Lund University Phone: +46 (0) 76 8585 706 Fax: +46 (0) 46 222 47 10 Ole Römers väg 1 (P.O. Box 188) SE-221 00 Lund, Sweden Web address: www.maxlab.lu.se Email: maria.hakans...@maxlab.lu.se __
Re: [ccp4bb] Unexplained electron density
Dear All, I have refined these atoms as water with half occupancy. I have a ligand in the solution and most of the half occupied water molecules form a cluster close to this ligand which is bound to my protein but not at full occupancy. The B-values are between 9 and 15 for 0.5 occupied water but my guess is that it is not water but ligand with an alternative conformation I see. I will do new experiments increasing the ligand concentration of my crystals to see if I could increase the occupancy and see it more clearly. Best regards Maria 22 Sep 2008 kl. 14:19 skrev Eleanor Dodson: First check - look for anom peaks. If your S atoms are showing up in the Dano map, them you can check whether this is a compound with S in it. crystallisation and cro- protectants contain a wealth of small molecules which often bind Eleanor 9 sigma peaks are rarely due to multiple site waters.. Eleanor Borhani, David wrote: Maria, 1.7 A is too long for common diatomic molecules (N2, 1.1 A; O2, 1.2 A; CO, 1.1 A) or molecules like hydrogen peroxide (~1.48 A), methanol (ditto), etc. Does the water have unusually low temp. factors (i.e., it's really a much heavier atom, and the peak you see is a Fourier ripple)? It may be indeed that you have (one) water at two alternate positions, but I think you need to reset to nothing modeled to be certain of density interpretaion moving forward. Thus, try removing the water you have already built, any surrounding waters or other ligands, and also the protein atoms to which all these are hydrogen bonded (set occ = 0), refine a few cycles, and then look at the diff. maps. Dave David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [EMAIL PROTECTED] 212-478-0698 http://www.deshawresearch.com -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Maria Håkansson Sent: Friday, September 19, 2008 8:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Unexplained electron density Hello David and others, Thanks for yur comments. I guess it might be as simple as water molecules, present in the structure but not at the same time. The density looks like a rod with uneven distribution. Both ends of the rods (1.7-1.8 Å in between) make hydrogen bonds to protein or other water molecules - normal distances (2.3-3.3 Å). Could it be strong water molecules but with partial occupancy meaning that both sites are occupied but not at the same time? I guess refmac automatically refines the molecules that way although I have not specified it in my file. So after refinement as too close water molecules there is no clash just nice density. However I assume it is appropriate to specify these water molecules as the same water but with an alternative conformation in the pdb file. Best Regards, Maria 19 Sep 2008 kl. 11:10 skrev David Briggs: Hi Maria, Initial questions: 1) What's present in crystallisation/purification buffers? 2) Are any other ligand visible for the 9sigma peak? 3) Does the 9 sigma peak also have a peak in an anomalous difference map? Assuming 1.7A is accurate (and with 1.5A resolution, you'd hope it would be!) a metal-ion - water interaction is looking less likely. Take a look at Marjorie Harding's papers and website for target metal ion - ligand distances, and the closest you'll see is water:Mg2+, at 2.07. http://tanna.bch.ed.ac.uk/newtargs_06.html So one would assume it is a covalently bonded compound. So back to question 1. What's in your buffers? A quick search for bond length tables suggests Carbon-Sulphur (1.8) and Carbon-Chlorine at 1.7. hope this helps David 2008/9/19 Maria Håkansson [EMAIL PROTECTED]: Hello All, I have a problem with a 9 sigma positive peak 1.7 Å away from a water molecule (or what I believe is a water molecule). There are several similar peaks in my map though only one is as high as 9 sigma. My first thought was to exclude these too close waters. However the R-values increased by more than 0.5 %. Could it be carbonmonoxide or oxygen atoms? By the way, It is 1.5 Å resolution data. Any suggestions? Best Regards, Maria Håkansson Maria Håkansson, Ph.D. tel: +46 (0) 76 8585 706 Senior Scientist, Max-lab, Lund University fax: +46 46 222 47 10 Ole Römers väg 1 (P.O. Box 188) www.maxlab.lu.se SE-221 00 Lund, Sweden [EMAIL PROTECTED] -- David C. Briggs PhD Father Crystallographer http://drdavidcbriggs.googlepages.com/home AIM ID: dbassophile Maria Håkansson, Ph.D. tel: +46 (0) 76 8585 706 Senior Scientist, SARomics Biostructures ABfax: +46 46 19 12 77 Scheelevägen 22 (P.O. Box 724) www.saromicsbiostructures.com SE-220 07 Lund, Sweden [EMAIL PROTECTED] Maria Håkansson, Ph.D. tel: +46 (0) 76 8585 706 Senior Scientist, SARomics Biostructures ABfax: +46 46 19 12 77 Scheelevägen 22
Re: [ccp4bb] Unexplained electron density
Hello David and others, Thanks for yur comments. I guess it might be as simple as water molecules, present in the structure but not at the same time. The density looks like a rod with uneven distribution. Both ends of the rods (1.7-1.8 Å in between) make hydrogen bonds to protein or other water molecules - normal distances (2.3-3.3 Å). Could it be strong water molecules but with partial occupancy meaning that both sites are occupied but not at the same time? I guess refmac automatically refines the molecules that way although I have not specified it in my file. So after refinement as too close water molecules there is no clash just nice density. However I assume it is appropriate to specify these water molecules as the same water but with an alternative conformation in the pdb file. Best Regards, Maria 19 Sep 2008 kl. 11:10 skrev David Briggs: Hi Maria, Initial questions: 1) What's present in crystallisation/purification buffers? 2) Are any other ligand visible for the 9sigma peak? 3) Does the 9 sigma peak also have a peak in an anomalous difference map? Assuming 1.7A is accurate (and with 1.5A resolution, you'd hope it would be!) a metal-ion - water interaction is looking less likely. Take a look at Marjorie Harding's papers and website for target metal ion - ligand distances, and the closest you'll see is water:Mg2+, at 2.07. http://tanna.bch.ed.ac.uk/newtargs_06.html So one would assume it is a covalently bonded compound. So back to question 1. What's in your buffers? A quick search for bond length tables suggests Carbon-Sulphur (1.8) and Carbon-Chlorine at 1.7. hope this helps David 2008/9/19 Maria Håkansson [EMAIL PROTECTED]: Hello All, I have a problem with a 9 sigma positive peak 1.7 Å away from a water molecule (or what I believe is a water molecule). There are several similar peaks in my map though only one is as high as 9 sigma. My first thought was to exclude these too close waters. However the R-values increased by more than 0.5 %. Could it be carbonmonoxide or oxygen atoms? By the way, It is 1.5 Å resolution data. Any suggestions? Best Regards, Maria Håkansson Maria Håkansson, Ph.D. tel: +46 (0) 76 8585 706 Senior Scientist, Max-lab, Lund University fax: +46 46 222 47 10 Ole Römers väg 1 (P.O. Box 188) www.maxlab.lu.se SE-221 00 Lund, Sweden [EMAIL PROTECTED] -- David C. Briggs PhD Father Crystallographer http://drdavidcbriggs.googlepages.com/home AIM ID: dbassophile Maria Håkansson, Ph.D. tel: +46 (0) 76 8585 706 Senior Scientist, SARomics Biostructures ABfax: +46 46 19 12 77 Scheelevägen 22 (P.O. Box 724) www.saromicsbiostructures.com SE-220 07 Lund, Sweden [EMAIL PROTECTED]
[ccp4bb] Unexplained electron density
Hello All, I have a problem with a 9 sigma positive peak 1.7 Å away from a water molecule (or what I believe is a water molecule). There are several similar peaks in my map though only one is as high as 9 sigma. My first thought was to exclude these too close waters. However the R- values increased by more than 0.5 %. Could it be carbonmonoxide or oxygen atoms? By the way, It is 1.5 Å resolution data. Any suggestions? Best Regards, Maria Håkansson Maria Håkansson, Ph.D. tel: +46 (0) 76 8585 706 Senior Scientist, Max-lab, Lund University fax: +46 46 222 47 10 Ole Römers väg 1 (P.O. Box 188) www.maxlab.lu.se SE-221 00 Lund, Sweden [EMAIL PROTECTED]
