Re: [ccp4bb] what to do with disordered side chains
On 4/4/2011 2:15 PM, Jacob Keller wrote: I like your IMGATM proposal, but wouldn't it also potentially break some of the programs? That depends on the program. Programs I write that read PDB files silently ignore keywords that they don't recognize. A model with IMGATM (or whatever keyword you standardize on) records would be interpreted as those those dummy atoms don't exist. If a program died because of them, or if the PDB consumer wanted to see the dummy atoms the keywords could be replaced with ATOM using a text editor and a global substitute, and the user would be aware that there is something different about those atoms. I would hope programs would be modified to do sensible things with the dummy atoms since they would have a clear indication that the atoms are indeed dummy. For a graphics program, maybe the bonds involving dummy atoms could be drawn a half brightness. They would be visible but clearly more ghost-like than the majority of atoms in the model. A refinement program could strip them out, perform the refinement, and rebuild them at the end, if needed, using WASNIAHC. I expect they would also be ignored completely in MR and homology modeling/comparison programs. In fact, pretty much any use I would make of the PDB file would involve discarding all the dummy atoms, but with this scheme I could at least know for sure which atoms are fantasy and which were build based on density. Also--and this is a problem with deleting only sidechain atoms in general--it seems that many, myself included, might totally miss that an apparent alanine is really a trunco-lysine. What I like is that it does get around the problem of people over-interpreting bogus sidechains, but it falls short, perhaps, in misleading people about what residue is there. I, for one, would not feel that I had to click on all the alanines in a model to verify that they were not lysines, and would be surprised and puzzled for a while about why this ala said lys when I clicked on it. Wouldn't you be surprised? (Well, maybe not after this thread...) I am surprised any time I see all the atoms in a lysine on the surface. What could possibly be holding that thing in place? is what jumps to my mind. When I see a side chain on the surface that ends at CB or CG I just assume it is something long and waving in the breeze. I guess it all depends on what you are used to looking at. With dummy atoms that are clearly labeled as such then the graphics programs can be programed as I described above and we both would have the visual cues that we desire. Another advantage of keeping the dummy flag separate from the occupancy and B factor fields is that these are then free to be used in the way they were intended. Numerous times I have built side chains that are visible to their end, but a second conformation ends at the CG. I split these side chains into A and B parts with a complete A and a partial B and the group occupancies of A and B sum to 1.0. Now if you tell me that I have to build the entire B side chain and must flag the dummy atoms with occ=0.0 we have a problem. For the dummy atoms the occupancies don't sum to 1.0 any more. Logic tells me that the occupancy of the dummy atoms should be the same as all the real B atoms. This particular case is a good example of why I don't like the idea of building complete side chains in the absence of density. If you are going to build out my B conformation you have to recognize that the reason I don't see density beyond the CG is that there is a B and C conformation for the next CD atom (remember I already have an A conformation for CD elsewhere). To make a logically complete side chain I need to build two dummy conformations for this residue and split my real CG, CB, and CA B conformation atoms with no way to decide the relative occupancies of the B and C conformations. That's a lot of complexity for a blurry bit of density. Hell, I have every reason to expect that there is a D conformation in there too - do I have to build that as well? If you expect such a shrub to be built for every surface lysine the IMGATM keyword and the program WASNIAHC would allow it to be generated and represented in an unambiguous and minimally confusing fashion. I wouldn't be happy having to add imaginary atoms to my models, but the representation meets my criteria, and I think it meets yours too. Dale Tronrud JPK On Mon, Apr 4, 2011 at 1:55 AM, Dale Tronruddet...@uoxray.uoregon.edu wrote: The definition of _atom_site.occupancy is The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. When an atom has an occupancy equal to zero that means that the atom is NEVER present at that site - and that is not what you intend to say. Setting the occupancy to zero does not mean that a full atom is located somewhere in this area. Quite the
[ccp4bb] PhD studentship in Structural Molecular Biology at Leeds Oct 2011
Dear BB, Please forward to any potential PhD applicants. Thanks Ed PhD studentship in Structural Molecular Biology in collaboration with AstraZeneca. Part of an integrated approach to discovering cell-permeable inhibitors of alpha helix-mediated protein-protein interactions. See http://www.bmb.leeds.ac.uk/staff/tae/AZ_Studentship_inStrucBiol_Ad.pdf For details. Supervisory team: Dr Thomas Edwards, Dr Andy Wilson, Professor Adam Nelson and Dr Stuart Warriner. Protein−protein interactions (PPIs) mediate many biological mechanisms, and, potentially, represent exciting targets for the treatment of disease. Although small molecule inhibitors of a few PPIs have been discovered, the principles that underpin the discovery of such ligands, within the boundaries of drug-like chemical space, are much less well established than for conventional medicinal chemistry targets such as enzymes and receptors. In addition, it is unlikely, for example, that current small molecule collections are honed for screening against PPIs. We will target three contrasting α-helix mediated PPIs of strategic interest to AZ. The proposed programme will integrate the combined expertise of the team at Leeds (and our collaborators at AZ) in the synthesis of both helix mimetics, and small molecules of unprecedented scaffold diversity, in combination with cutting edge structural biology. The studentship will start by October 1st 2011 and the stipend would be at the standard research council rate (~ £13,895 pa for 2011/12). Applications, for this 3.5 year studentship which will be accepted until the studentship is filled, should be directed to Anna Luty, School of Chemistry, University of Leeds, Leeds LS2 9JT and can be made online via the following link: http://www.chem.leeds.ac.uk/postgraduate-research/how-to-apply.html Please contact Dr Thomas Edwards (t.a.edwa...@leeds.ac.uk) or Dr. Andy Wilson (a.j.wil...@leeds.ac.uk) for further details about this project. UK Research Council eligibility rules apply. __ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ -- There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact. ~Mark Twain
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
hello if u are getting merged spot then try to increase detector distance it may work . instead of this u try to reduce delta phi (gonimeter phi angle per frame) default it is 1 degree u can try 0.5, 0.25 degree.
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Hi Deng, On Tue, 2011-04-05 at 07:31 +0200, Poul Nissen wrote: Deng, You need a good synchrotron source with a low point spread detector, but not least a careful consideration in crystal mounting so that your crystal rotates apprx around the long axis during data collection to optimise the separation of reflections on the detector If you go to a beamline that has a goniostat with a kappa axis you will be able to orient the long axis of your crystal after mounting to minimise overlaps. You don't say where you are located, but there are quite a number of beamlines that are suitable for this kind of work in Europe. I am not so familiar with the instrumentation available at MX beamlines in the USA, but I believe that there are possibilities there as well. Regards, Peter. besides checking that the long axis is not a result of bad cryo and crystal deterioration during flash cooling Poul On 05/04/2011, at 07.05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987 -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Hi Vandana, in addition to the hints already mentioned some experimental setups offer the posiblitiy to swing out the detector via a theta-angle option. this might be useful when increasing the crystal-to-detector distance to avoid overlaps. Cheers, Georg Am 05.04.11 11:20, schrieb vandana kukshal: hello if u are getting merged spot then try to increase detector distance it may work . instead of this u try to reduce delta phi (gonimeter phi angle per frame) default it is 1 degree u can try 0.5, 0.25 degree. -- Universität Tübingen Interfakultäres Institut für Biochemie Dr. Georg Zocher Hoppe-Seyler-Str. 4 72076 Tuebingen Germany Fon: +49(0)-7071-2973374 Mail: georg.zoc...@uni-tuebingen.de http://www.ifib.uni-tuebingen.de
[ccp4bb] Data Strategy for anisotropic diffraction
Dear all, i am new in the field and my crystals give anisotropic pattern. I would really appreciate if someone who has experience with data collection with anisotropy diffraction to recommend relative literature on data strategy concerning anisotropy. Cheers, Alex
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Hi dengzq1987, You don't say how many axes are long. I will assume one. In that case, here is a compilation of what others have already recommended, with some additions: 1. Orient the crystal so that the long axis is along the rotation axis. It can be done during mounting the crystal on the loop or, if the goniostat is equipped with multi-axis goniometer, then after mounting your crystal on the goniometer. But try to pre-orient your crystal as much as you can when scooping it. 2. Increase sample to detector distance: It can help but it will not work if your long axis is along the beam. Overlaps in that case will be more function of the frame width. In that case, see 3. 3. Decrease the angular range measured in a single frame: It will alleviate the problem not solved in 2. When you do that, you may have to also decrease the exposure per image using less intense beam and/or less exposure time. Otherwise, you radiation dose per degree of data will increase killing you crystal before you collect complete data. 4. Find the detector with a smaller point spread function. 5. Find a synchrotron beamline with a smaller beam. 6. Find a synchrotron beamline with less divergent beam. Keep in mind, that some times (but NOT ALWAYS), 5 and 6 are mutually exclusive. 4, 5, and 6 will have less effect than 1, 2 and 3. Good luck! Nukri -Original Message- From: CCP4 bulletin board on behalf of dengzq1987 Sent: Tue 4/5/2011 12:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Ideally you should rotate your crystal around the long axis during data collection. This is however easier said than done since often such crystals grow a plates with the long axis perpendicular to the plane of the plate. As long as the long axis is more or less oriented perpendicular to the x-ray beam (+/-45 deg but depending on the severity of the case) you will get away with it and you might even consider large oscillation ranges. For orientations with the long axis in a direction close to the X-ray beam, you will have to reduce the oscillation range, perhaps even to 0.1deg to avoid excessive spot overlap. Here things depend heavily on mosaicity, which should be low (preferably 0.2 deg). Otherwise spots may always overlap, even on still images. Very often (in my experience at least) crystals with one particularly long axis have high symmetry, and collecting a large wedge covering the good orientations can be sufficient. Of course I don't know if you are that lucky. If you are not sure which part to collect, collect at least 180 deg to be sure you covered the whole unique part of reciprocal space. BTW, you didn't say what is long. My post extreme case until now was P3121 with a=b= 50, c = 360 and this resulted in very good 2.4 A data from a rystal with mosaicity 0.1-0.15. Crystals with mosiacity around 1.0 deg were useless because of too much overlap. Remy Op 5/04/2011 7:05, dengzq1987 schreef: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some /direction/ the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
For plate crystals with the long axis normal to the plate surface (anecdotally, this is usually the case), you can use bent loops. Bent loops can be made using tweezers by folding over the loop onto the stem and crimping with the tweezers. When the loop relaxes a bit, it will leave a ~90deg-bent loop, so the crystal can sit on the loop and be shot edge-on in the beam. It takes a bit of time to get it right, but it worked well for me one time. JPK On Tue, Apr 5, 2011 at 7:29 AM, Jürgen Bosch jubo...@jhsph.edu wrote: What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] disulfide bond question
I have a question related to protein structure, but not crystallography per se. Has anyone see a disulfide forming between the two cys of CXC in the middle of a loop, and create a sharp turn, where X is not a proline? I seems to me that geometrically this would be possible but I am not sure how stable it is, or how energetically unfavorable it might be. thanks so much for your input! Ronnie
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Hampton Research actually sells bent loops. At least used to. Raji On Tue, Apr 5, 2011 at 8:52 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: For plate crystals with the long axis normal to the plate surface (anecdotally, this is usually the case), you can use bent loops. Bent loops can be made using tweezers by folding over the loop onto the stem and crimping with the tweezers. When the loop relaxes a bit, it will leave a ~90deg-bent loop, so the crystal can sit on the loop and be shot edge-on in the beam. It takes a bit of time to get it right, but it worked well for me one time. JPK On Tue, Apr 5, 2011 at 7:29 AM, Jürgen Bosch jubo...@jhsph.edu wrote: What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- --- Raji Edayathumangalam Research Fellow in Neurology, Harvard Medical School Postdoctoral Fellow, Center for Neurologic Diseases, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
my crystal is not plate.it is Hexagonal and very large. 2011-04-05 dengzq1987 发件人： Jacob Keller 发送时间： 2011-04-05 20:53:41 收件人： CCP4BB 抄送： 主题： Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? For plate crystals with the long axis normal to the plate surface (anecdotally, this is usually the case), you can use bent loops. Bent loops can be made using tweezers by folding over the loop onto the stem and crimping with the tweezers. When the loop relaxes a bit, it will leave a ~90deg-bent loop, so the crystal can sit on the loop and be shot edge-on in the beam. It takes a bit of time to get it right, but it worked well for me one time. JPK On Tue, Apr 5, 2011 at 7:29 AM, Jürgen Bosch jubo...@jhsph.edu wrote: What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
You may have a fairly long cell edge (or two if you are dealing with P3 or P6), but you also seem to have high mosaicity (pic spot 1). Try the useful strategies suggested here. It may also be worthwhile to shoot a few roomtemp crystals to see if your cryo is at fault for your high mosaicity. Bert On 4/5/11 9:10 AM, dengzq1987 dengzq1...@gmail.com wrote: hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 发件人： Jürgen_Bosch 发送时间： 2011-04-05 20:29:18 收件人： dengzq1987 抄送： CCP4BB@JISCMAIL.AC.UK 主题： Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
XDS should be able to help you with this it's not terribly overlapping and 3D profile fitting does wonders. Jürgen On Apr 5, 2011, at 9:10 AM, dengzq1987 wrote: hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 发件人： Jürgen_Bosch 发送时间： 2011-04-05 20:29:18 收件人： dengzq1987 抄送： CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK 主题： Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.commailto:dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987 sopt 2.JPGspot 1.JPG .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Pictures are helpful to narrow the range of recommendations. It would be even more helpful to see the entire image, to know the orientation of the rotation axis, detector distance used, frame width, and any other information on the setup you can provide. Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dengzq1987 Sent: Tuesday, April 05, 2011 8:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 发件人： Jürgen_Bosch 发送时间： 2011-04-05 20:29:18 收件人： dengzq1987 抄送： CCP4BB@JISCMAIL.AC.UK 主题： Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
On Tue, 2011-04-05 at 13:05 +0800, dengzq1987 wrote: I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? With denzo, a useful trick in this situation at the integration stage is to use really small spot radius combined with large background radius. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
From the two images, it appears there are two short cell axes and one long axis - it also looks like trigonal or hexagonal, then the long axis should be c. Of course lower symmetry with a nearly hexagonal-shaped cell can not be ruled out. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1 On 5 Apr 2011, at 15:24, Van Den Berg, Bert wrote: You may have a fairly long cell edge (or two if you are dealing with P3 or P6), but you also seem to have high mosaicity (pic spot 1). Try the useful strategies suggested here. It may also be worthwhile to shoot a few roomtemp crystals to see if your cryo is at fault for your high mosaicity. Bert On 4/5/11 9:10 AM, dengzq1987 dengzq1...@gmail.com wrote: hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 发件人： Jürgen_Bosch 发送时间： 2011-04-05 20:29:18 收件人： dengzq1987 抄送： CCP4BB@JISCMAIL.AC.UK 主题： Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some direction the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
In the first image (spot 2) the long unit cell is obvious from the closely spaced spots, but this kind of image can be handled easily by Denzo. The second one (spot 1), although at first glance the spots seem well separated, is the problem. As Bert pointed out the mosaicity is high, so the lunes are overlapping (you don't see separate rings or crescents where Ewalds sphere intersects different layers of the lattice). That means the apparently individual spots are multiple spots one on top of the other, with the long axis nearly perpendicular to the plane of the picture. This means there is no information about the spacing of the long axis in this picture,and the picture is rather insensitive to rotation, so integration is likely to get lost unless you fix these parameters. If you fix the parameters based on the good orientation and integrate on through, you will be sampling the lattice rods at intervals (as the 2D electron crystallographers say) rather than measuring discreet spots. However if you collect while rotating around the long axis, you will never see this orientation and should have no serious problem. eab dengzq1987 wrote: hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 *发件人：* Jürgen_Bosch *发送时间：* 2011-04-05 20:29:18 *收件人：* dengzq1987 *抄送：* CCP4BB@JISCMAIL.AC.UK *主题：* Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com mailto:dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some /direction/ the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05 dengzq1987
[ccp4bb] Postdoc position at University of Konstanz
Postdoc position at University of Konstanz Interested candidate please write to Prof Wolfram Welte, wolfram.we...@uni-konstanz.de. A post doctoral position is available instantly at the University of Konstanz in a collaborative EU project (FP7). The position is limited to February 2012. A six month extension may be possible. We are looking for a person who has thorough experience in molecular biology, i.e. particularly genetic techniques and biochemistry. The designated person will work on the construction of DARPINS for three membrane protein complexes. Part of the work will be carried out in the lab of Andreas Plückthun at the University of Zurich. Please submit your application letter by email including curriculum vitae, a brief description of previous research experience to Prof Wolfram Welte Fachbereich Biologie Universität Konstanz D-78457 Konstanz Germany eMail: wolfram.we...@uni-konstanz.de http://strucbio.biologie.uni-konstanz.de/strucbio/ Puneet Juneja University of Konstanz
Re: [ccp4bb] disulfide bond question
Ronnie, There are several. The example I know is 1DBI - I have little doubt that there are more out there... If you are interested by the close proximity in sequence then you might also like to know that there are examples of 'CC' motifs with disulfides - look at 1KB0 - a PQQ-dependant alcohol dehydrogenase by Oubrie et al. - Allister Crow John Innes Centre On 05/04/2011 13:55, Ronnie wrote: I have a question related to protein structure, but not crystallography per se. Has anyone see a disulfide forming between the two cys of CXC in the middle of a loop, and create a sharp turn, where X is not a proline? I seems to me that geometrically this would be possible but I am not sure how stable it is, or how energetically unfavorable it might be. thanks so much for your input! Ronnie
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
dengzq1987, I am also working on a data set that has this exact alignment/mosaicity problem noted by others. If you make a movie of your dataset that displays your images in series, or if you just click through them quickly in adxv or your program of choice, you will see that very few of the spots ever leave their positions on the detector as you rotate the crystal. This demonstrates the mosaicity issue described by Bert and Ed. In my case, Denzo seems to be able to properly measure the a and b axes of my hexagonal cell (I know this based on a comparison of these values to structures of homologs in the same SG), but tells me that my c axis is only 0.21A. It seems to me that in the case of overlaps, the dimensions of the corresponding axis would be overestimated rather than seriously underestimated (0.21A!), so I'm not really sure of what is going on here. Maybe someone who knows more about the software could shed some light on this crazy measurement? I've been told by a few people that XDS may be able to handle this dataset, but I haven't gotten to trying it yet. I'll work on it today or tomorrow and follow up if I have any success. Best, Mike - Original Message - From: Edward A. Berry ber...@upstate.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, April 5, 2011 8:38:17 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? In the first image (spot 2) the long unit cell is obvious from the closely spaced spots, but this kind of image can be handled easily by Denzo. The second one (spot 1), although at first glance the spots seem well separated, is the problem. As Bert pointed out the mosaicity is high, so the lunes are overlapping (you don't see separate rings or crescents where Ewalds sphere intersects different layers of the lattice). That means the apparently individual spots are multiple spots one on top of the other, with the long axis nearly perpendicular to the plane of the picture. This means there is no information about the spacing of the long axis in this picture,and the picture is rather insensitive to rotation, so integration is likely to get lost unless you fix these parameters. If you fix the parameters based on the good orientation and integrate on through, you will be sampling the lattice rods at intervals (as the 2D electron crystallographers say) rather than measuring discreet spots. However if you collect while rotating around the long axis, you will never see this orientation and should have no serious problem. eab dengzq1987 wrote: hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 *发件人：* Jürgen_Bosch *发送时间：* 2011-04-05 20:29:18 *收件人：* dengzq1987 *抄送：* CCP4BB@JISCMAIL.AC.UK *主题：* Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer distance. Don't rotate 1degrees but take 1/2 of the mosaicity. Obviously you want to make good use of the detector area so adjust the edges to where your crystal really diffracts. And if that resolution leads to too many overlaps then limit your resolution and get first a good datasets home. You then can play with 2theta for a higher resolution dataset. Another obvious thing to do and you don't mention what reduction program you use is to let XDS sort your problem out. Unless you collected to high resolution without being cautious XDS could help. If not, well then you had your experience and now should know better. SSRL has options to collect 450 A cells to 3A without much hassle. That was my largest cell so far. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Apr 5, 2011, at 1:05, dengzq1987 dengzq1...@gmail.com mailto:dengzq1...@gmail.com wrote: hello all, does anyone have the experience of Collecting Data from Long Unit Cell Axes ? I have a crystal that diffracts to about 4 A. in some /direction/ the spots overlap. we can't use the data to index .we think it is because that there is a long unit cell axes. so is there any method to solve this problem? best wishes. 2011-04-05
Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?
Thanks for the explanation Ed, that makes sense. - Original Message - From: Edward A. Berry ber...@upstate.edu To: mi...@chem.ucla.edu Cc: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, April 5, 2011 12:22:21 PM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? When the c axis is perpendicular to the image, i.e. parallel to the xray beam, the only information about spacing along the c axis comes from the distance between the lunes. There should be a circle of spots around the direct beam with l=0, the a clear space, then a ring with l=1, then a clear space, then a ring with l=2 and so on. As the c dimension gets longer, the layers get closer together in reciprocal space, and these rings caused by intersection of the l-planes with Ewald's sphere get closer together. As the mosaicity increases, reflections whose centers are farther from ewalds sphere will be in diffraction, and the rings get broader. In the extreme of long c axis and/or high mosaicity the rings overlap completely and there appears to be only one circle of spots around the direct beam center extending out to the diffraction limit. Presumably denzo takes this to be the l=0 layer, and since it can't find the l=1 layer assumes it is out of the picture beyond the diffraction limit, which would be the case if you had an extremely short c axis so the layers are far separated. So it can get a good fit to the spot using correct a, b and a very small c. eab mi...@chem.ucla.edu wrote: dengzq1987, I am also working on a data set that has this exact alignment/mosaicity problem noted by others. If you make a movie of your dataset that displays your images in series, or if you just click through them quickly in adxv or your program of choice, you will see that very few of the spots ever leave their positions on the detector as you rotate the crystal. This demonstrates the mosaicity issue described by Bert and Ed. In my case, Denzo seems to be able to properly measure the a and b axes of my hexagonal cell (I know this based on a comparison of these values to structures of homologs in the same SG), but tells me that my c axis is only 0.21A. It seems to me that in the case of overlaps, the dimensions of the corresponding axis would be overestimated rather than seriously underestimated (0.21A!), so I'm not really sure of what is going on here. Maybe someone who knows more about the software could shed some light on this crazy measurement? I've been told by a few people that XDS may be able to handle this dataset, but I haven't gotten to trying it yet. I'll work on it today or tomorrow and follow up if I have any success. Best, Mike - Original Message - From: Edward A. Berryber...@upstate.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, April 5, 2011 8:38:17 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? In the first image (spot 2) the long unit cell is obvious from the closely spaced spots, but this kind of image can be handled easily by Denzo. The second one (spot 1), although at first glance the spots seem well separated, is the problem. As Bert pointed out the mosaicity is high, so the lunes are overlapping (you don't see separate rings or crescents where Ewalds sphere intersects different layers of the lattice). That means the apparently individual spots are multiple spots one on top of the other, with the long axis nearly perpendicular to the plane of the picture. This means there is no information about the spacing of the long axis in this picture,and the picture is rather insensitive to rotation, so integration is likely to get lost unless you fix these parameters. If you fix the parameters based on the good orientation and integrate on through, you will be sampling the lattice rods at intervals (as the 2D electron crystallographers say) rather than measuring discreet spots. However if you collect while rotating around the long axis, you will never see this orientation and should have no serious problem. eab dengzq1987 wrote: hello Jürgen_Bosch, because i have collected the data,but can't index.in some direction,the spot is separated .but the others are set close together(picture spot1 and spot 2).so we think there is one long unit cell axes. 2011-04-05 dengzq1987 *发件人：* Jürgen_Bosch *发送时间：* 2011-04-05 20:29:18 *收件人：* dengzq1987 *抄送：* CCP4BB@JISCMAIL.AC.UK *主题：* Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ? What do you consider long ? 200, 300 ? 600 A ? Before shooting try to run strategy or xplan. Move the detector back to first reliably be able to determine your cell. Then double your estimated mosaicity and see what strategy suggests. If you don't get many overlaps (5%) then try a closer
Re: [ccp4bb] disulfide bond question
Ronnie -- The list that I have in a home database contains 89 instances of a CXC in 53 files when C-C forms a disulfide bond. The records returned are ordered by the name of X residue from CXC motif for convenience. There is indeed PRO in one case (2zxt), but it is not the major observation in CXC motif. hope this helps cheers -- heping pdbid | resn-X |chainids| resseq ---+-++ 1xm7 | ALA | A, B |156 1zp0 | ALA | B |162 2blf | ALA | A |244 2bpb | ALA | A |244 2c9x | ALA | A |244 2ca3 | ALA | A |244 2ca4 | ALA | A |244 2b5g | ARG | B, A |121 3bj8 | ARG | B, A |121 2bcf | ASN | A |101 1dbi | ASP | A |138 1wrj | ASP | A | 30 3inj | CYS | E |302 1ssu | GLN | A | 20 3me2 | GLU | R |126 3me4 | GLU | A, B |126 3nzy | GLU | B, D |126 1jr8 | GLY | B, A |110 1jra | GLY | B, D, C, A |110 2bxr | GLY | B, A |322 3i8i | GLY | 4 | 17 3i9c | GLY | 4 | 17 3lvt | GLY | A |355 2he8 | HIS | A, B | 6 2ipg | HIS | B, A | 6 2p5n | HIS | A, B | 6 3cv6 | HIS | A, B | 6 3fac | HIS | B | 6 3fjn | HIS | A, B | 6 1z3s | ILE | B, A |434 1z3u | ILE | A, B, C, D |434 2gy7 | ILE | A |434 2irm | LEU | A | 52 1cx8 | PHE | G, B, F, H, D, C, A, E |557 1de4 | PHE | F, C, I|557 1ewk | PHE | A, B |290 1ewt | PHE | B, A |290 1ewv | PHE | B, A |290 1isr | PHE | A |290 1iss | PHE | B, A |290 1suv | PHE | B, A |557 1t3n | PHE | B |830 2nsu | PHE | A, B |557 3lmk | PHE | A, B |277 2zxt | PRO | A |397 1mec | SER | 3 | 87 1nhr | SER | A | 41 1tmf | SER | 3 | 88 2mev | SER | 3 | 87 3dxu | SER | A |311 2a4h | THR | A | 81 2ozk | VAL | C, A |291 2w8n | VAL | A |341 (53 rows) On 05/04/2011 13:55, Ronnie wrote: I have a question related to protein structure, but not crystallography per se. Has anyone see a disulfide forming between the two cys of CXC in the middle of a loop, and create a sharp turn, where X is not a proline? I seems to me that geometrically this would be possible but I am not sure how stable it is, or how energetically unfavorable it might be. thanks so much for your input! Ronnie
Re: [ccp4bb] disulfide bond question
Hi Heping, Thanks for the list. It is very helpful and interesting. Out of curiosity: how did you generate this list? Is there a way to search none-linear motifs in PDB? Or did you write a script for searching database? BTW, the ALA in 1xm7 looks unreal. A three-way tri-sulfide? The electron density for the C155 seems too weak to support the C155-C157 linkage. Guess this one should not be counted. Zhijie -- From: Heping Zheng d...@iwonka.med.virginia.edu Sent: Tuesday, April 05, 2011 5:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] disulfide bond question Ronnie -- The list that I have in a home database contains 89 instances of a CXC in 53 files when C-C forms a disulfide bond. The records returned are ordered by the name of X residue from CXC motif for convenience. There is indeed PRO in one case (2zxt), but it is not the major observation in CXC motif. hope this helps cheers -- heping pdbid | resn-X |chainids| resseq ---+-++ 1xm7 | ALA | A, B |156 1zp0 | ALA | B |162 2blf | ALA | A |244 2bpb | ALA | A |244 2c9x | ALA | A |244 2ca3 | ALA | A |244 2ca4 | ALA | A |244 2b5g | ARG | B, A |121 3bj8 | ARG | B, A |121 2bcf | ASN | A |101 1dbi | ASP | A |138 1wrj | ASP | A | 30 3inj | CYS | E |302 1ssu | GLN | A | 20 3me2 | GLU | R |126 3me4 | GLU | A, B |126 3nzy | GLU | B, D |126 1jr8 | GLY | B, A |110 1jra | GLY | B, D, C, A |110 2bxr | GLY | B, A |322 3i8i | GLY | 4 | 17 3i9c | GLY | 4 | 17 3lvt | GLY | A |355 2he8 | HIS | A, B | 6 2ipg | HIS | B, A | 6 2p5n | HIS | A, B | 6 3cv6 | HIS | A, B | 6 3fac | HIS | B | 6 3fjn | HIS | A, B | 6 1z3s | ILE | B, A |434 1z3u | ILE | A, B, C, D |434 2gy7 | ILE | A |434 2irm | LEU | A | 52 1cx8 | PHE | G, B, F, H, D, C, A, E |557 1de4 | PHE | F, C, I|557 1ewk | PHE | A, B |290 1ewt | PHE | B, A |290 1ewv | PHE | B, A |290 1isr | PHE | A |290 1iss | PHE | B, A |290 1suv | PHE | B, A |557 1t3n | PHE | B |830 2nsu | PHE | A, B |557 3lmk | PHE | A, B |277 2zxt | PRO | A |397 1mec | SER | 3 | 87 1nhr | SER | A | 41 1tmf | SER | 3 | 88 2mev | SER | 3 | 87 3dxu | SER | A |311 2a4h | THR | A | 81 2ozk | VAL | C, A |291 2w8n | VAL | A |341 (53 rows) On 05/04/2011 13:55, Ronnie wrote: I have a question related to protein structure, but not crystallography per se. Has anyone see a disulfide forming between the two cys of CXC in the middle of a loop, and create a sharp turn, where X is not a proline? I seems to me that geometrically this would be possible but I am not sure how stable it is, or how energetically unfavorable it might be. thanks so much for your input! Ronnie
Re: [ccp4bb] Data Strategy for anisotropic diffraction
Alex, You should check out this webserver: http://services.mbi.ucla.edu/anisoscale/ If it cannot solve your problem, it will at least point you in the direction of some answers. Good luck, Mike - Original Message - From: Alex Barth alexbart...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, April 5, 2011 4:11:18 AM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] Data Strategy for anisotropic diffraction Dear all, i am new in the field and my crystals give anisotropic pattern. I would really appreciate if someone who has experience with data collection with anisotropy diffraction to recommend relative literature on data strategy concerning anisotropy. Cheers, Alex -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
