Re: [ccp4bb] Unidentified density
hi sudhir, i think in second snapshot you can fit MPD as its structure is seems similar. . On Fri, Feb 10, 2012 at 11:36 AM, Sudhir Kumar sudhir.1...@gmail.comwrote: Dear all, I have a 2 A structure of an enzyme which show 12 molecules per asymmetric unit. While placing waters i found out some blobs where i could not model any ligand. It is surrounded by 3 Asp molecules. I have attached screenshot of the blob at 1.5 sigma cutoff 2fo-fc density. Crystallization condition had following precipitants: PEG 1000, Peg 3350, MPD, Ethylene glycol,and protein contained Glycerol. My protein is known to bind Cysteine/Serine, though i haven't added any in crystallization buffer. any suggestion what it might be are welcome. thanks in advance -- best regards Sudhir Kumar Research Scholar C/O Dr. S. Gourinath Structural Biology Laboratory SLS, JNU, New Delhi-110067 -- Vandana kukshal
Re: [ccp4bb] Dye for protein affinity measurement
Hi, - If ur protein is making strong complex then You can run Native page with increasing concentration of your inhibitor peptide and decrease in complex band intensity will show you competitive binding of your inhibitor to proteins. - You can do ELISA... by coating one of your protein ad then add second protein and then detect by using antibodies against second protein ... with increasing concentration of peptide or inhibitor signal should go down. - if interaction is weak then design a peptide (part of protein B ) which definitely binds to protein with Alexa , or FITC labelled and do interaction study by observing the change in fluorescence. and if interaction is there do assay with different inhibitors ... On Wed, Feb 8, 2012 at 8:13 PM, Xiaodi Yu uppsala@hotmail.com wrote: Hello Jiahong: If I understand correctly that you want to test protein-protein interaction or inhibition study in solution, maybe you can try something like ELISA to test protein-protein interaction. Or if your B protein has 6 histag, you can use Ni-NTA agrose beads to test inhibition or binding depending on your purpose. And another option (a little dangerous ), is using radio active to label one of your protein. Yu Xiaodi -- Date: Wed, 8 Feb 2012 14:17:47 + From: patr...@douglas.co.uk Subject: Re: [ccp4bb] Dye for protein affinity measurement To: CCP4BB@JISCMAIL.AC.UK Jiahong Thermo sells a series of kits called DyLight Fluor for fluorescent labelling of antibodies or other proteins. They have everything you need and they're very convenient and easy to use. You can pick the excitation and emission wavelength. If you label both A and B (or C) with different colors you will be able to see if both are in your crystals (assuming crystallization is part of your approach). You need only label a small percentage of your protein or peptide to see whether the protein is present in a crystal. Patrick http://en.wikipedia.org/wiki/DyLight_Fluor Forsythe, E.L., Achari, A., and Pusey, Marc L. (2006), Trace Fluorescent Labeling for High Throughput Crystallography, Acta Cryst. D62, 339-346. We used DyLight 350 NHS Ester to check we had protein crystals - see methods section of *Cryst. Growth Des.*, 2011, *11* (8), pp 3432–3441 2012/2/8 Jiang Jiahong jiang_jiah...@126.com Dear all, I am looking for some kind of dye for protein affinity comparison, but do not know which to choose. I know protein A can contact B to form a complex,now I hope to find something simiar with A to act as an inhibitor to block the process of A-B complex formation. Maybe a short peptide, a segment of protein A or even some organic molecule. Because here is a poor access to ITC nor Biacore, I can only rely on some dye to check the competence between A and inhibitor candidates. If any one can offer any suggestions. That would be so grateful! Any way,thank kind-hearted people in advance! Regards Jiahong -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- Vandana kukshal
Re: [ccp4bb] a PDB tool
Dear You just have to renumber the residue in coot and save or renumbering can be done in ccp4 edit pdb module in coordinate utilities. On Tue, Jan 3, 2012 at 5:52 PM, Dialing Pretty hdc123hdc...@yahoo.comwrote: Dear All, I have a PDB file starting from residue 1 to 100 for example, can you introduce me a server so that I can convert it to another PDB file starting from 200 to 300? Cheers, Dialing -- Vandana kukshal
Re: [ccp4bb] How to add add atoms by Coot
hi pretty , Once when u will fit the atom in green density (+ve Fo-Fc map) (Green density means there is some thing missing and you need to model) You need to refine the structure by using refinement program. while refining the structure program will calculate Fc and then again it will generate map by calculating Fo-Fc if your atom is properly fitted Fo-Fc will go down and green density will disappear. So first refine the structure and then again see the density for those atoms. regards On Wed, Jan 4, 2012 at 10:51 AM, Dialing Pretty hdc123hdc...@yahoo.comwrote: Dear All, Attached is a Screenshot of coot. The blue is the 2FoFcwt map, the green is the FoFcwt map. After I select the FoFcwt map, I have tried to change the green blob to an atom. First I point a green blob, then I use calculate-Model/Fit/Refine-Pointer Atom Type to add any atom. My question is, although the atom can be added, there is no indication that the volume of the green blob changes. If I am right, the green blob should disappear if the atom is correctly selected. How do you solve this problem? How about the red blobs in the attached Screenshot? I am looking forward to getting your reply. Cheers, Dialing -- Vandana kukshal
Re: [ccp4bb] Hydrophobic interactions
Dear amit sir you can go through this server .. http://pic.mbu.iisc.ernet.in http://pic.mbu.iisc.ernet.in/index.html . PIC server can calculate many interactions within and between the protein molecules. ..PIC: Protein Interactions Calculator K. G. Tina, R. Bhadra, and N. Srinivasan,NAR 2007 best regards On Thu, Dec 15, 2011 at 2:04 AM, Luthra,Amit alut...@uchc.edu wrote: Hi Everyone I have to calculate hydrophobic interactions in pdb files. Is any server available for this type of calculation? ** ** Thanks in advance ** ** Amit -- Vandana kukshal
Re: [ccp4bb] How can improve diffraction quality
Hello You can do dehydration of crystal to get better diffraction ...go through this reference Dehydration Converts DsbG Crystal Diffraction from Low to High Resolution Begoña Herashttp://www.sciencedirect.com/science?_ob=RedirectURL_method=outwardLink_partnerName=27983_origin=article_zone=art_page_linkType=scopusAuthorDocuments_targetURL=http%3A%2F%2Fwww.scopus.com%2Fscopus%2Finward%2Fauthor.url%3FpartnerID%3D10%26rel%3D3.0.0%26sortField%3Dcited%26sortOrder%3Dasc%26author%3DHeras,%2520Bego%25C3%25B1a%26authorID%3D6603651310%26md5%3Dd2d49a88c2751086c775153e3331f609_acct=C60364_version=1_userid=3424920md5=6dbc863b94c3bf6340f12da6adee70a8 1 http://www.sciencedirect.com/science/article/pii/S096921260354#AFF1 , Melissa A. Edelinghttp://www.sciencedirect.com/science?_ob=RedirectURL_method=outwardLink_partnerName=27983_origin=article_zone=art_page_linkType=scopusAuthorDocuments_targetURL=http%3A%2F%2Fwww.scopus.com%2Fscopus%2Finward%2Fauthor.url%3FpartnerID%3D10%26rel%3D3.0.0%26sortField%3Dcited%26sortOrder%3Dasc%26author%3DEdeling,%2520Melissa%2520A.%26authorID%3D6603262033%26md5%3Dd57707bf83335a312588ce73d3bd730b_acct=C60364_version=1_userid=3424920md5=4d0dd88d8b5e3162c388c8da007533b6 1 http://www.sciencedirect.com/science/article/pii/S096921260354#AFF1 , Karl A. Byrielhttp://www.sciencedirect.com/science?_ob=RedirectURL_method=outwardLink_partnerName=27983_origin=article_zone=art_page_linkType=scopusAuthorDocuments_targetURL=http%3A%2F%2Fwww.scopus.com%2Fscopus%2Finward%2Fauthor.url%3FpartnerID%3D10%26rel%3D3.0.0%26sortField%3Dcited%26sortOrder%3Dasc%26author%3DByriel,%2520Karl%2520A.%26authorID%3D6701558759%26md5%3D8cc9cd028d7292811a47d9ccd3e6d9a4_acct=C60364_version=1_userid=3424920md5=95f75e9e035dbb96b2ac2458638a7acf 1 http://www.sciencedirect.com/science/article/pii/S096921260354#AFF1 , Alun Joneshttp://www.sciencedirect.com/science?_ob=RedirectURL_method=outwardLink_partnerName=27983_origin=article_zone=art_page_linkType=scopusAuthorDocuments_targetURL=http%3A%2F%2Fwww.scopus.com%2Fscopus%2Finward%2Fauthor.url%3FpartnerID%3D10%26rel%3D3.0.0%26sortField%3Dcited%26sortOrder%3Dasc%26author%3DJones,%2520Alun%26authorID%3D8156858700%26md5%3D992099f5dce064695b2b201c7ef62fa0_acct=C60364_version=1_userid=3424920md5=5b36006773491de6f1fe3e11fd3f0362 1 http://www.sciencedirect.com/science/article/pii/S096921260354#AFF1 , Satish Rainahttp://www.sciencedirect.com/science?_ob=RedirectURL_method=outwardLink_partnerName=27983_origin=article_zone=art_page_linkType=scopusAuthorDocuments_targetURL=http%3A%2F%2Fwww.scopus.com%2Fscopus%2Finward%2Fauthor.url%3FpartnerID%3D10%26rel%3D3.0.0%26sortField%3Dcited%26sortOrder%3Dasc%26author%3DRaina,%2520Satish%26authorID%3D7005284671%26md5%3D339a4d07d0c405b35ede6cc65bd10b4a_acct=C60364_version=1_userid=3424920md5=d179172315a3ce2212b520bd72cedf71 2 http://www.sciencedirect.com/science/article/pii/S096921260354#AFF2 , Jennifer L. Martinhttp://www.sciencedirect.com/science?_ob=RedirectURL_method=outwardLink_partnerName=27983_origin=article_zone=art_page_linkType=scopusAuthorDocuments_targetURL=http%3A%2F%2Fwww.scopus.com%2Fscopus%2Finward%2Fauthor.url%3FpartnerID%3D10%26rel%3D3.0.0%26sortField%3Dcited%26sortOrder%3Dasc%26author%3DMartin,%2520Jennifer%2520L.%26authorID%3D8043271300%26md5%3Dbfbb451581631e88eb9aab78dba30ce2_acct=C60364_version=1_userid=3424920md5=28050987b73ecd02a369b5486c0d6ce0 1 http://www.sciencedirect.com/science/article/pii/S096921260354#AFF1 , Structure, Vol. 11, 139–145, February, 2003, On Tue, Oct 18, 2011 at 5:52 PM, Charles Allerston charles.allers...@sgc.ox.ac.uk wrote: Silver bullet Additive screens Methylation Construct boundaries in situ proteolysis Have you got a ligand? Stick in in there! Do you have an expression tag? Cleave it/leave it on. What is in your protein buffer? Mess about with that? Temperature gradients How is your purity? How quickly are you getting this in to trays? Can you speed this up? Might be a factor. Annealing at the beamline? etc. cheers, charlie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Afshan Begum [afshan...@yahoo.com] Sent: 18 October 2011 12:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How can improve diffraction quality Dear ccp4 user I am facing one crucial problem regarding diffraction. Actually the size of my crystal is good enough 0.5mm but it was diffracted only 4 A. The conditions of crystallization recipes are 4.5% PEG 1000, 0.1M Tris and 25mM Na citrate. I really need your suggestions regarding how can i improve my diffraction quality? Your support is highly appreciable. Best Regards AFSHAN -- Vandana kukshal
Re: [ccp4bb] data processing problem with ice rings
Hello , Can any one send me pdf of this paper as its a old paper and not accessible here . M.F. Perutz, Preparation of haemoglobin crystals. *J. Cryst. Growth* , * 2 * (1968), pp. 54–56. On Fri, Oct 14, 2011 at 10:42 AM, ChenTiantian chentiantian2...@gmail.comwrote: Hi there, I am processing a dataset which has bad ice rings (as you can see in the attach png file). I tried both XDS and imosflm, and got similar results, it seems that adding EXCLUDE_RESOLUTION_RANGE cannot get rid of the effects of the ice rings. the following is part of the CORRECT.LP which is the second attached file, you can find more details there. SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 4.24 371525537 5545 99.9% 46.9% 52.7% 371502.4850.8%19.4% -28% 0.5135136 3.01 553449002 9840 91.5% 62.7% 65.1% 551161.7668.3%48.1% -28% 0.5207760 2.46 84636 12699 12703 100.0% 67.4% 84.7% 846341.5573.0%54.2% -19% 0.513 12104 2.13 97910 14743 14987 98.4% 254.5%199.3% 979080.16 276.2% 4899.9% -23% 0.473 14037 1.90 110260 16846 16940 99.4% 299.2%303.3% 1102450.06 325.0% -99.9% -17% 0.422 15995 1.74 118354 18629 18744 99.4%1062.0% 1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 1.61 122958 20193 20331 99.3% 967.5% 1571.1% 1228680.10 1059.7% 987.3%-2% 0.402 18348 1.51 125075 21554 21794 98.9% 838.9% 1355.1% 1249330.08 922.6% 1116.9%-1% 0.402 18977 1.42 72057 17042 23233 73.4% 640.8% 775.3%703910.08 732.5% 826.7%-8% 0.425 10003 total 823746 136245144117 94.5% 166.4%166.7% 8215620.40 181.1% 296.7% -15% 0.435 119774 Note that I/SIGMA of each resolution shell is 2.5, so how should I do to process the dataset properly? Any suggestion about this super ice rings? Thanks! Tiantian -- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Shanghai, 201203 -- Vandana kukshal
Re: [ccp4bb] stoichiometry of complex and incubator
Hi , yes as *Konstantin* said if u have cysteine residue in ur any one of protein u can label that protein with Pyrene malemide or oregon malemide or other fluorescence dye then remove the dye by desalting column. titrate with second protein and do fluorescence anisotropy experiment to get the KD value (stochiometry). one more thing u can do. u can add kinase motif in one of ur protein by re-cloning and then label with labelled ATP and then do EMSA with other protein. regards On Thu, Aug 4, 2011 at 9:13 AM, Konstantin v. Korotkov k...@u.washington.edu wrote: Hi Min, If your proteins have cysteine residues, or you could introduce them into the sequence, then you could label the interacting proteins with a fluorescent label, run an SDS-PAGE and quantify the bands with a fluorescent scanner. See for example Supplementary Figure 1C in Fronzes et al. (2009) Science 323: 266. -Konstantin On Wed, 3 Aug 2011, m zhang wrote: Dear all, I have two unrelated questions. Any suggestion on any of them will be greatly appreciated. First, we have two proteins that bind each other without a doubt. But since we have very limited amount of proteins and it takes a long time to reproduce them, we are very hesitating to try ITC and AUC to find out the stoichiometry of these complex. So I am wondering if there is any other way we can try to find the ratio without consuming much proteins? Second, we are thinking about getting a new incubator for crystallization. Could anyone here recommend a model or a brand? Thank you, Min -- Konstantin Korotkov, Ph.D. Research Scientist University of Washington Department of Biochemistry Box 357742 Seattle, WA 98195-7742 (206)616-4512 k...@u.washington.edu -- -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
[ccp4bb] mising atoms
hello, i have one problem regarding electrostatic field calculation . in a PDB with 2 A resolution many atoms of side chan if argenine and aspartate , lysine and glutamate are missing due to weak electron density . i want to calulate the field how should i go for it . if i ll build the side chain atom is this wil be correct way to do these calculation. welcome ur valuable sugessions . -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures
hi , in CCP 4 package u can run CONTACT program use NCONT to find symmetry contacts only. u can Fix contact distance minimum and maximum also . On Thu, Jul 14, 2011 at 5:18 PM, sukanta mondal sukanta.mon...@gmail.comwrote: I know, in PyMOL using 'symexp' possible to generate symmetry related molecules for a given crystal structure. But I'm looking for some program/software (for batch) by which I can find out the number of symmetry related molecules (distance cutoff = 5A) interacting with a given chain in a crystal structure. Thanking you, suku NIBIO, Osaka -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
Re: [ccp4bb] B factor
hello sir , in chimera its available in module Render by Attribute. go through this link http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html . regards On Fri, May 13, 2011 at 12:01 AM, Luthra,Amit alut...@uchc.edu wrote: Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
Re: [ccp4bb] about the working solution
Hi i also faced this type of problem with my protein. i used additive screen for getting some thick needles and then with that condition i used seeding approach to get thick single crystal. try to use micro seeding with this . i used micro dilution or streak seeding for this. for seeding try to get that condition in which crystals come late..try to play with precipitant concentration for this ... regards 2011/4/26 xinghua qin xtal...@gmail.com hi,everyone, Sorry for the off-topic question.I got two many crystals in the drop with long thin needle shape and crossed , after optimization, no big change appeared, and I got only a few needle clusters in the drop at most times. which one is better for next optimization step and suitale to be the working solution? In my opinion, the latter one has fewer nucleus, but the former one has better shape, did I got the point? Best wishes Xinghua Qin -- Xinghua Qin Room 4022, Center for Life Sciences, China Agricultural University, No.2, Yuan Ming Yuan West Road, Haidian District， Beijing，China，100193 Tel: +86-10-62732672 -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
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] metal binds?
yes u can run Native page and on that if u will see shift then crystals containing heavy atom regards On Fri, Mar 25, 2011 at 1:09 PM, Careina Edgooms careinaedgo...@yahoo.comwrote: Dear ccp4 users I would like to know, is there a way to check that heavy metal has bound to crystals before I take it to synchrotron which is far away? thanks Careina -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy Aruna Asaf Ali Marg 110 067 New Delhi INDIA
Re: [ccp4bb] determining the domain for overexpression and crystallization
yes limited proteolysis is the best choice for the domain determination of unknown protein from our lab some people did this. after doing limited proteolysis just sequence digested part N terminally or the C terminally and find out the region from where its getting digested. side by side u can do fold prediction using phyre or u can use fold index to know the compact part of the protein. go through J Biol Chem. http://www.ncbi.nlm.nih.gov/pubmed/18974091 2008 Dec 26;283(52):36532-41. Epub 2008 Oct 30. Characterization of Rv3868, an essential hypothetical protein of the ESX-1 secretion system in Mycobacterium tuberculosis. Luthra Ahttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Luthra%20A%22%5BAuthor%5D , Mahmood Ahttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Mahmood%20A%22%5BAuthor%5D , Arora Ahttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Arora%20A%22%5BAuthor%5D , Ramachandran Rhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Ramachandran%20R%22%5BAuthor%5D . did similar work . On Fri, Mar 18, 2011 at 4:19 AM, Xianhui Wu wuxian...@gmail.com wrote: Dear all, Thank you very much for all of information about domain determination! I think the limited proteolysis is a good choice for the domain determination as we have no information about a protein. However, if we do have a domain information by the bioinformatics, how can we truncate the domain? Are we need to keep three or five more amino acids in two ends? Thanks. Best regards, Xianhui On Tue, Mar 8, 2011 at 2:22 AM, Mark J van Raaij mjvanra...@cnb.csic.eswrote: for an experimental way to determine soluble domains see the following paper: ESPRIT: an automated, library-based method for mapping and soluble expression of protein domains from challenging targets. Yumerefendi H, Tarendeau F, Mas PJ, Hart DJ. J Struct Biol. 2010 Oct;172(1):66-74. Epub 2010 Mar 4. Review. PMID: 20206698 [PubMed - indexed for MEDLINE] 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 7 Mar 2011, at 19:18, gauri misra wrote: Hi, To start with it would be great if you look in to the secondary structure prediction of the sequence using any of the standard servers like PSIPRED, JPRED etc. Many more available at expasy site http://ca.expasy.org/tools/. Whatever construct you finally choose to make just remember the standard rule that we generally follow is to avoid deleting the alpha helices and beta sheets. You can design your initial primers so as to obtain the complete amplification of these secondary structures from any part within the protein. You can even use the various modules of the following online available server http://scratch.proteomics.ics.uci.edu/ to have an idea of the intrinsically disordered regions in the protein, transmemebrane regions and disulfide bonds that would certainly help you in initiating in the right direction. Best wishes Gauri On Mon, Mar 7, 2011 at 4:10 AM, Xianhui Wu wuxian...@gmail.com wrote: Dear all, Before we try to study the crystal structure of an unknown protein, we need to determine the sequence that can fold into a compact and stable 3D domain. What kinds of methods can we choose? -- Best regards, XH Wu -- Best regards, Xianhui -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy Aruna Asaf Ali Marg 110 067 New Delhi INDIA
[ccp4bb] Fwd: [ccp4bb] use of beta-mercaptoethanol in crystallization
hi sreetama, if ur protein is making aggregates during crystallization try to add glycerol, EDTA in Ur buffer. R u purifying ur protein from Gelfiltration column ?is ur protein is coming in proper place? if every thing is right then u can try DTT and TCEP in ur buffer instead of Beta mercaptoethanol. for one of my crystallization experiment i used 1- 10 mM of Beta mercaptoethanol. -- vandana kukshal CSIR-senior research fellow X ray lab ,MSB division central drug research institute lucknow -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy Aruna Asaf Ali Marg 110 067 New Delhi INDIA
[ccp4bb]
hello sir , recently i have collected one data of 3.0 A of a protein having no sequence homology with any known PDB . but while fold prediction i got 100 % identical fold with some of the protein . space group of my protein is P622 and showing 6 molecule in a assymetric unit. the homologous fold proteins are trimer protein. can i run MR in this case . how i should proceed. i m trying for MIR also . regards vandana
[ccp4bb] covalent bond
how to make covalent bond between ligand and protein residue by using CCp4 package
[ccp4bb]
i have one Query . after using phenix auto build for building model R factor and R free reduced but B factor is increesed for all the atom .what next i should do to decrease the B factor of atoms.
[ccp4bb]
hello this is not a new question i was searching this in archives but i did'nt get . just send me link for this . i want to link AMP covalently with lysine in my structure (phosphoamide bond)how i will do this in coot and refmac . in turbo there is option make bond but in this no option is there . thanx
[ccp4bb] multi domain protein
i have one query. that if we have a multi domain protein structure to solve ,and we know about only one small domain of the protein for MR . other domain structure is not known then how we can proceed. is there any procedure to utilize phase from the solution with known domain .
[ccp4bb] multi domain protein
hello i have 3.25 A data of multidomain protein with 4 individual domain .one domains structure is already known . and for others domain 40 % simmilar structure is known . when i am running phaser with one known domain i am getting the solution but after getting solution i am serching other domains but clashes are coming . how should i proceed . thanx
[ccp4bb]
hi i am solving one structure in which after refinement i got R factor=27 and R free =27.7 i want to know that is it correct or i did some over refinment the Resolution is 3.0 A
[ccp4bb]
i am using restrain refmac for refine ment and coot for fiting its resolution range is 116.248 -3.00 number of used reflections 20215 the R factor is 27.7 and R free is 27.0 and if i am doing further restrain refinement with 0.03 geometry weight R factor is going down to 25.5 but R free is increasing to 30.5 should i go for further refinemnet
