[ccp4bb] Postdoctoral position in Case Western Reserve University
*Post-doctoral Research fellowship position available for crystallographer/protein chemist with molecular biology experience **at the CCMSB, Case Western Reserve University.* Requirements: • PhD in Biochemistry, Biophysics, Chemistry, Molecular Biology or similar • Significant experience in protein structure determination using X-ray crystallography • The individual should have the ability to manage projects and deadlines • Good technical and troubleshooting skills The Center for membrane and structural biology is well-equipped with core facilities including: x-ray diffraction, NMR, EM, mass spec, crystallization robots, ITC and fluorescence spectroscopy. The salary will be determined based on the experience of the candidate. CWRU is an equal opportunity employer. Send your resume to Chris Dealwis on *cxd...@case.edu <cxd...@case.edu>* For more information please visit: *http://pharmacology.case.edu/department/faculty/primary/Pages/dealwis.aspx* <http://pharmacology.case.edu/department/faculty/primary/Pages/dealwis.aspx> *https://www.ncbi.nlm.nih.gov/pubmed/?term=Chris+Dealwis* <https://www.ncbi.nlm.nih.gov/pubmed/?term=Chris+Dealwis> -- Intekhab Alam
[ccp4bb] modelling a flexible peptide
Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] change in unit cell parameters and difficult MR
Hi all I have collected 2 datasets; one for the native proteins (2.3Å resolution) while other is for a protein-protein complex (3.5Å resolution). The unit cell parameters for the native are a=120, b=196, c=109, a=g=90, b=114, while for the complex data it is a=122, b=197, c=300, a=g=90, b=93. I have successfully got a MR solution and refined the native dataset with 3 monomers in the asymmetric unit. Analysis of the protein complex dataset shows 41% pseudo translation and so far there is no success in molecular replacement for this dataset. Can anyone please suggest me ways to solve this problem. i already have tried different templates like monomer, dimer, trimer, tetramer etc with truncations of loop region. i am using phaser as well as molrep programs. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] unidentified density
Thanks to the members for responding to my queries. I would like to summarize the post as: 1.Improve the crystals to have a better dataset. 2. Poly A/G modelling to improve the density and then model the sequence. 3. use of secondary structure prediction tools and docking the sequence accordingly. 4. use of buccaneer. i will post again once i get a reasonable model. regards intekhab alam On Fri, Feb 10, 2012 at 8:58 PM, Eleanor Dodson c...@ysbl.york.ac.ukwrote: On 02/10/2012 07:35 AM, intekhab alam wrote: Hi all I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density. I want to model the aminoacid having sequence as given peptide: MGKKGKNKKGRGRPGVFRTRGLTDEEYDEF**KKRRESRGGKYSIDDYLADREREEELLERD** EEEAIFGDGFGLE 1.Based on map features which segemnt should i start with. 2. Is there anyway that i can build the best fit segment of my second protein. I tried autobuild but it failed to build any peptide for my second protein. Your help is highly appreciated. regards Try buccaneer - it should work very easily with that density.. Eleanor -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] brainpool research associate position
Dear members Have a look on the advertisement for the position of research associate in structural biology. Interested candidates please reply to kh...@korea.ac.kr. Informal enquiries can also be made. Structural Bioinformatics Lab, Department of Biotechnology Bioinformatics, Korea University, Seoul Korea Brainpool Research Associate – Full time, fixed term appointment for up to two years The Structural Bioinformatics Lab is seeking a Brainpool Research Associate to carry out structural analysis (x-ray crystallography) and biophysical studies of complexes related to virus-host interaction. The group is led by Professor Kyung Hyun Kim and has over the years produced good results (PNAS, NAR, JGV). The research programme is funded by a grant from the Korean Federation of Science and technology Societies (www.brainpool.or.krhttps://mail.google.com/mail/html/compose/static_files/www.brainpool.or.kr) to which both the applicant and our team apply together. Further details on the research group can be found at http://sbl.korea.ac.kr/. Applicants should have a PhD in Structural Biology, Biophysics or a related area, with at least 5 years of research experience after Ph.D., or high profile publications in the highest impact journals. Salary range will be from $45,000-$55,000 per annum plus plane ticket, moving expense and medical insurance. Initial salary for possibly the two months will be dependent on the skills and experience of the successful applicant. Closing date for completed applications: 5 February 2012. To apply for this position please send emails to kh...@korea.ac.kr with your resume. Korea U is an equal opportunities employer and encourages applications from all candidates irrespective of gender, race, disability, sexual orientation, age, religion and belief or another protected characteristic. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] strange MR problem
Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] MR problem
Hi there I have a data of heterotrimer protein complex at 2.9A resolution. One protein consists of two domains. I tried phaser as well as molrep which gives a solution with only one domain. Rotation function and translation function were found to be fine for these solutions. I tried to find missing domain of the protein after fixing one of the domain or the other partner proteins using whole part or various truncations of missing domain. I also tried to find and build missing domain using Rosetta with the solutions of Molrep or Phaser as template. But, there were no solutions, or the solutions are clashed with other domain or proteins. Furthermore, R and Rfree is 30 and 40, respectively, and I could not reduce them further. There was almost no electron density map in the empty space so that I could not model manually. Plz guide me ,how can i look for the missing domain in the protein. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] protein aggregation
Hi I think glycerol 10% or higher is a good choice. I have some experience with a protein that started aggregation beyond 2.5mg/ml. I tried crystallisation at this concentration with protein ligand ratio of 4:1 and was successful. On Thu, Mar 24, 2011 at 4:29 AM, vikrant saa powervikr...@yahoo.co.inwrote: Dear Gauri This may be the saturation point of your protein and beyond this it will start precipitating in a particular buffer. Try to set the crystallization trial (if it is your application ) and select those condition in which you see clear drop. Change the purification buffer with that condition buffer. It may work .. Else you can use Sucrose (0.5-2M), PEG6000 (5-10%), glycerol (5-10%) etc in different combination. all d best ** *Vikrant *** --- ***Senior Research Fellow (CSIR) * *Varma Lab* *Cancer Research Institute Advance Centre for Treatment, Research and Eduction in Cancer (ACTREC) Tata Memorial Hospital, Kharghar, Navi Mumbai-410210 * -- *From:* gauri misra kamga...@gmail.com *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Wed, 23 March, 2011 11:11:55 PM *Subject:* [ccp4bb] protein aggregation Hi, What are the different methods to prevent protein aggregation while concentrating so as to increase the concentration of the protein? I have some idea of adding EDTA and charged amino acids like L-Arg and L-Glu. I would appreciate if the readers share their experiences. Thanks! Gauri -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] exo and endo conformation
Hi there i have modeled a ribavirin molecule in one of the structures that i solved at 2.5A recently. omit map confirms the presence of ligand but the map itself is not very clear.there is some positive density in fo-fc map around the ribose ring, that disappears at 3.2sigma level. I wonder whether it is possible that the ribose ring has exo(2' and 3') and endo(2' and 3') conformation in the model. from where can i get the coordinates of these conformations of ribavirin. or how can i draw this using sketcher in ccp4. can anyone please send me the smileys of these two conformations. any other suggestions are also welcome. regards and thanks in advance, -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] SC
I want to calculate the shape comlementarity statitics (SC) of a dimeric protein using CCp4. I am using CCP4 6.1.3 on windows but the SC program is not available in that suite. Which version of CCP4 has that program. Are there any other programs that can calculate that. Thanks -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] pseudotranslation in C2 space group
Hi, There 1.I have collected two data sets one for the native protein (60Kda) and complex of native with other protein of 8 Kda. The shape of native dataset is cubic while that of the complexed one is triangular. A number of dataset were collected for these two and i successfully indexed them to a spacegroup of C2. 2.While doing molecular replacement for the native data using a monomeric template clear solution with 3 monomers in the asyymetric unit was obtained and structure solved successfully with R/rfee of 19/23 at 2.5A reolution. 3.The molecular replacement of the complexed dataset with the same template gave a solution with 2 monomers in asymmetric unit with a lot of clashes between the two subnuints. when i closely examined the logfile i observed that there was pseudotranslation detected by the program in all of my complex dataset. I run xtiage as well as pointless and truncate which rules out any twinning as well as wrong space group assignment. Pseudotranslation of 18% has been detected by balbes. 4. I also run the Balbes at Murshodov server which gave a solution with 4 monomers in the asymmetric but still showing a lot of clashes in the asymmetric unit (R/Rfree 0.43/0.47) followed by automatic refinemnet with Arp/wARp which gave a model . When i examine the density of the model i saw a lot of clashes in the asymmetric unit but the density are interpretable so that bakbone can be easily modelled. But the R and R free donot goes down from (R/Rfree 0.43/0.47) I have pasted the logfile below from molrep for your convenience. Kindly suggest me how can i proceed with this dataset. That will be very kind of you if you spend some time over my problem. Another question , is it possible that this pseudotranslation is due to the smaller protein of the complex which has slightly changed the crystal packing. ( SDS done on the complex crystals clearly showed the presence of both the proteins). --- Check Patterson for pseudo-translation --- PST_limit : 0.125 of origin peak INFO: pseudo-translation was detected. Origin Patterson peak: P,P/sig : 80563.180 266.237 1 Patterson. peak: p,P/sig : 80560.719 266.228 2 Patterson peak : P,P/sig : 13992.70846.242 3 Patterson peak : P,P/sig : 13992.70846.242 Peak 1: trans.vector /ort/ :60.16498.423 0.000 trans.vector /frac/: 0.500 0.500 0.000 Peak 2: trans.vector /ort/ :31.861 0.000 0.000 trans.vector /frac/: 0.265 0.000 0.000 Peak 3: trans.vector /ort/ :28.30398.423 0.000 trans.vector /frac/: 0.235 0.500 0.000 INFO: translation vector of peak 2 will be used. WARNING: with keyword: PST -- MODE = F , STICK = N Sol_ Space group : C 1 2 1 Sol_ No: 5 Sett: 2 Sol_ Cell: 120.328 196.846 109.285 90.00 113.84 90.00 Sol_--- Rotation function --- Sol_ Radius of gyration : 23.58 Sol_ Radius of integration : 47.16 Sol_ Resmin,Resmax : 48.032.42 WARNING: For this radius integration program uses data included between48.0 and2.71 (angstrom..) --- rfcoef for model --- --- rfcoef for Fobs --- NCS (from Self rotation Function): 1 NCS_model (from Model Self rotation Function): 1 Program will use NCS_model =: 1 Number of RF peaks : 30 thetaphi chialphabeta gamma Rf Rf/sigma Sol_RF 1 106.45 50.401.37 320.211.31 39.410.9325E+05 19.98 Sol_RF 2 0.000.000.000.000.000.000.8668E+05 18.57 Sol_RF 3 158.10 -1.79 120.96 209.61 37.87 33.180.8147E+05 17.46 Sol_RF 422.21 -179.07 120.40 149.19 38.30 327.330.7596E+05 16.28 Sol_RF 5 0.83 144.00 179.87 143.941.66 35.930.4234E+05 9.07 Sol_RF 6 146.73 90.95 73.37 329.03 38.27 327.140.3574E+05 7.66 Sol_RF 7 0.000.00 179.92 97.160.00 82.760.3504E+05 7.51 Sol_RF 834.01 88.19 71.45 29.00 38.12 32.610.3354E+05 7.19 Sol_RF 977.12 174.71 90.84 97.45 87.95 288.040.2136E+05 4.58 Sol_RF 10 134.42 132.297.11 39.815.07 315.220.2089E+05 4.48 Sol_RF 11 152.93 177.57 136.00 21.98 49.92 206.840.1861E+05 3.99 Sol_RF 12 156.31 -169.21 19.45 91.887.78 250.290.1849E+05 3.96 Sol_RF 13 130.28 116.07 92.63 351.98 66.96 299.830.1810E+05 3.88 Sol_RF 14 0.000.00 11.30 11.300.000.000.1808E+05 3.87 Sol_RF 1536.79 -89.11 90.53 219.84 50.36 218.060.1801E+05 3.86 Sol_RF 16 134.90 -102.85 173.11 82.03 90.00 107.720.1761E+05 3.77 Sol_RF 17 106.060.94 54.00 262.92 51.73 81.030.1753E+05 3.76 Sol_RF 18 135.11 85.04 162.00 277.64 88.39 287.56
[ccp4bb] Difference map
Hi Folks I have a query regarding the difference map between the two structures ligand bound data (2.5A) and native (2.8A). I tried to calculate the fourier difference map between two data sets ligand bound- native. The protocol in CCP4 that i used is as: 1.merge the mtz file of native nad ligand bound using cad 2. scaling this combine file with scaleit program followed by map generation uisng fft. I got the map but i did not find the fu;ll map of the ligand,i can only see small density nera the ligand binding site at 5 sigma level. I have calculated omit map that cleraly showed the ligand. why is such discrepency in the two cases, is there is something missing from the calculation. kindly help me out. Thanks and regards Intekhab alam -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] monomer-dimer
Hi everyone Sorry for some non specific query! i am working with a protein that shows a dimer in the crystal structure but when i tried to figure out that with standard molecular markers in gel filteration (superdex-200, 24ml column) it turned out to be a monnomer. Native gel analysis after incubating the protein at 20 degree, 37 degree showed more dimer at 20 degree celcius as compared to 37. I tried similar strategy in gel filteration by incubating my protein at various temperature,where a lot of precipitation was observed at 37 degree celcius and after removing the precipitates i run the gel filteration that has 0.5 ml higher elution volume as compared to samples incubated at 20 degree celcius and 4 degree celcius.( Is this significant) Furthermore i have done some experiments in cold room (4 degree) where the elution volume is stuck at a point irrespective of the conditions (as Flow rate, concentration of protein etc) and that is higher than that of the room temperature by 1 ml. Standard moleculr weight markers also show higher elution volume in cold room in comparison to the room temperature by 1 ml. I will be highly obliged if someone suggest some literature or any otherway to do gel filtrtaion so that i can clearly resolve this issue. Also let me know if there is some literature available on effect of temperature on the elution volume of proteins. Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] monomer-dimer
Dear That was a quite enlightening discussion!! I am grateful to you guys for your time!! I will definitily try some of these to get a clear answer. Regards Intekhab alam On Tue, Aug 10, 2010 at 8:38 AM, Bostjan Kobe b.k...@uq.edu.au wrote: Dear Intekhab Let me just add to this that gel filtration is not an accurate method for determination of molecular mass, because the migration on the column depends on the shape of the protein. The following methods can be used to determine molecular mass irrespective of shape: - MALLS (multi-angle laser light scattering or static light sxattering) - sedimentation equilibrium on analytical ultracentrifuge (AUC) - native mass spectrometry For a short recent review on issues associated with determining oligomeric state from crystal structures, with older references and relevant bioinformatic tools cited in there, please see http://www.ncbi.nlm.nih.gov/pubmed/19021571 Bostjan On 10/08/10 6:26 AM, Maia Cherney ch...@ualberta.ca wrote: To determine the oligomeric state of a protein (monomer or dimer in your case), it's useful to use the PISA server. You upload your pdb file from the crystal structure.The server calculates the areas of interfaces (buried area) and deltaG (change in Gibbs energy) upon oligomer dissociation. (E. Krissinel and K. Henrick (2007). /Inference of macromolecular assemblies from crystalline state/. J. Mol. Biol. *372*, 774--797 . E. Krissinel and K. Henrick (2005). /Detection of Protein Assemblies in Crystals/. In: M.R. Berthold /et.al./ (Eds.): CompLife 2005, LNBI 3695, pp. 163--174 http://dx.doi.org/10.1007/11560500_15. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303} If the interface area (divided by 2 per one protomer) is greater than 1000 A2 and delta G is more than 5kcal/mol (the higher the better), it's a dimer. However, don't forget that most dimers can dissociate into monomers upon dilution. There is a dynamic equilibrium between dimers (oligomers) and monomers that depends on their concentration and the Kdiss. Separating them in any method will disturb this equilibrium. If the re-equilibration time is greater than the separation time, you can see both monomers and dimers. You can even roughly calculate the dissociation constant: Kdiss=[monomer]2/[dimer] where brackets mean concentrations. To give you an estimate, at Kdiss=10(-3)M, you have roughly equal concentration of dimers and monomers at 10-3 M and only 10% dimers at 10-4 M. Sometimes, protein needs to dissociate easily for the biological function. Maia intekhab alam wrote: Hi everyone Sorry for some non specific query! i am working with a protein that shows a dimer in the crystal structure but when i tried to figure out that with standard molecular markers in gel filteration (superdex-200, 24ml column) it turned out to be a monnomer. Native gel analysis after incubating the protein at 20 degree, 37 degree showed more dimer at 20 degree celcius as compared to 37. I tried similar strategy in gel filteration by incubating my protein at various temperature,where a lot of precipitation was observed at 37 degree celcius and after removing the precipitates i run the gel filteration that has 0.5 ml higher elution volume as compared to samples incubated at 20 degree celcius and 4 degree celcius.( Is this significant) Furthermore i have done some experiments in cold room (4 degree) where the elution volume is stuck at a point irrespective of the conditions (as Flow rate, concentration of protein etc) and that is higher than that of the room temperature by 1 ml. Standard moleculr weight markers also show higher elution volume in cold room in comparison to the room temperature by 1 ml. I will be highly obliged if someone suggest some literature or any otherway to do gel filtrtaion so that i can clearly resolve this issue. Also let me know if there is some literature available on effect of temperature on the elution volume of proteins. Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail
[ccp4bb] molecular replacement
Hi all I am trying to do molecular replacement with low resolution (4Å) using Molrep and Phaser. Overall R-factor is 11.3%, completeness 95.4%, I/sigma 2, and Chi^2 0.95. Identities between my protein and templates were more than 80%. I couldn’t get correct solution. Rotation function, translation score, and contrast were low, and they had no significance, though I changed the range of resolution. Molrep suggested solution coordinates clashed with symmetry molecules. I tried MR after remove clashed regions, but another clashes happened. In the case of phaser, there were many clashes, too. Please, give me any suggestion. Should I concern about any options when I run MR programs? Hope you guys will be interested to answer!! Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] complex
Hello I am trying to complex two proteins of 57 and 18 kda and using pET 22b as an expression system. I purified both with His tag and the purity is quite nice after Ni-NTA (Buffer is Tris,Nacl and Imidazole). After purification with Ni_NTA i tried to improve my protein purity using gel filteration(superdex-200). I successfully got the 57 Kda with a high purity (Buffer is Tris and nacl) but with the smaller protein i didnt get anything after the column. when i tried dialysis to remove imidazole from this 18kda protein it degraded.i tried protease inhibitors as well but still the protein is not stabilised. Can anyone suggest me something to get out from this. I am stuck at this stage. suggestion are highly welcomed and appreciated. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] advertisemnet for the research scientist position in Korea
You are invited to apply for a brain pool scientist position in the field of structural biology under *Professor Kyung Hyun Kim of Korea University.* The research project will focus on the structure of viral infectious disease proteins and is funded by the *Brainpool initiative program of **Korean Federation of science and Technology Societies (KOFST)*. This program is funded initially for one year with a good remuneration package including the travel, living as well as relocating expenses. Minimum qualification is phd with 5 year research experience in the relevant field with impressive publications in the peer reviewed journals.For the more detailed information cruise through the website www.brainpool.or.kr. Interested applicants can ask for the initial enquiries directed to the email address or by telephonic contact number given below. The last date of the application is 25th May 2010 by 6 P.M. Kyung Hyun Kim, Professor Structural Bioinformatics Lab Korea University Sejong Campus Phone 82 2 3290 3444; Mobile 82 10 9014 1416 http://sbl.korea.ac.kr/ Email: kh...@korea.ac.kr -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
[ccp4bb] research position in korea
You are invited to apply for a brain pool scientist position in the field of structural biology under Professor Kyung Hyun Kim of Korea University. The research project will focus on the structure of viral infectious disease proteins and is funded by the Brainpool initiative program of Korean Federation of science and Technology Societies (KOFST). This program is funded initially for one year with a good remuneration package including the travel, living as well as relocating expenses. Minimum qualification is phd with 5 year research experience in the relevant field with impressive publications in the peer reviewed journals.For the more detailed information cruise through the website www.brainpool.or.kr. Interested applicants can ask for the initial enquiries directed to the email address or by telephonic contact number given below. The last date of the application is 25th May 2010 by 6 P.M. Kyung Hyun Kim, Professor Structural Bioinformatics Lab Korea University Sejong Campus Phone 82 2 3290 3444; Mobile 82 10 9014 1416 http://sbl.korea.ac.kr/ Email: kh...@korea.ac.kr
[ccp4bb] ligand modelling
Hi All I solved one structure of a viral RNA polymerase in complex with some ligands at 2.6 A resolution. The ploymerase structure has 3 monomers in the asymmetric unit and in all the 3 monomers i found |Fo|-|Fc| as well as 2Fo|-|Fc| map for the ligand. I tried to model my ligand there and after putting that some naegative density propped up outside the 2Fo|-|Fc| map and also the postive density inside the 2Fo|-|Fc| map didnt disappeared completely at 3 sigma (although it is reduced significantly). I tried putting metals and other things there but most of the positive density is gone only when i put my ligand there. Besides these the ligand fits well only in one of the three chains at 1 sigma while in rest two it is around 0.8 sigma of |Fo|-|Fc| map. I measured the B factor and findout that the B and C has higher B facors (33) as compared to A (29). can anyone suggest me about how to improve or fine tune my map around the ligand so that i can get rid of this positive and negative density (i already have tried different binding modes. Thanks -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
