Re: [ccp4bb] obtaining a difference of two columns in a mtz file
Arnon Lavie wrote: Hi - I would like to calculate the difference of two columns in a mtz file - specifically of the native and heavy atom structure factor columns. The difference should be in a new column. What is the easiest way of doing this? Arnon sftools will do this. Here is a script to calculate something different but a similar idea. #!/bin/csh -f # Run sftools to calculat I and SIGI from F and SIGF, and append results # Scale both by 0.001 # # # mtzdmp /y/people/ccp4/cadd/hipip.mtz # P21 # H K L FP SIGFP DANO SIGDANO sftools eof read /y/programs/xtal/ccp4-4.2.1/examples/toxd/toxd.mtz CALC J COL ITOXD3 = 0.001 COL FTOXD3 * COL FTOXD3 * CALC Q COL SIGITOXD3 = 0.002 COL FTOXD3 * COL SIGFTOXD3 * WRITE toxd+I.mtz END eof
[ccp4bb] moelcular replacement with large cell
Dears, I am doing molecular replacement of a protein complex with a P622 data set with large cell parameters (a=b=135, c=480). The data set seems well. R merge is 0.17 for all and 0.70 for the last shell of 2.9 angstrom. I am not sure it is a complex in the crystal. Phenix analysis reveal there is no twin. The proposed protein complex is about 70 kDa with a larger subunit of 50 kDa and a small subunit of 20 kDa. The matthews analysis indicates that there might be 3 complexes in the ASU. The structure of the 50 kDa subunit is known while the 20 kDa one is unknown. But molecular replacement failed with either Phaser or Molrep. Self-rotation with CNS reported the result as below: ! index, psi, phi, kappa, RF-function ( 0.25) 1 0.000 0.000 180.000 29.7217 Self-ratation with Molrep reported the result as below: Number of RF peaks : 30 thetaphi chialphabeta gamma Rf Rf/sigma Sol_RF 1 0.000.000.000.000.000.000.3444E+05 17.13 Sol_RF 290.00 -80.07 179.990.00 180.00 -19.86 5061. 2.52 Sol_RF 390.00 -65.53 179.990.00 180.00 -48.94 4890. 2.43 Sol_RF 490.00 -76.12 179.990.00 180.00 -27.76 4722. 2.35 Sol_RF 511.42 90.00 61.00 30.00 11.53 30.00 2438. 1.21 Sol_RF 6 164.38 60.00 179.99 60.00 -31.24 120.00 1850. 0.92 Sol_RF 785.13 -141.54 179.97 38.32 -170.26 141.40 1805. 0.90 Sol_RF 890.00 -60.00 90.00 30.00 -90.00 -30.00 1764. 0.88 Sol_RF 984.07 -144.87 179.96 34.98 -168.15 144.73 1743. 0.87 Sol_RF 1072.25 -60.00 89.30 46.76 -84.03 -13.24 1665. 0.83 Sol_RF 11 138.24 -130.77 180.00 49.23 83.52 130.77 1608. 0.80 Sol_RF 12 170.36 30.00 179.99 30.00 -19.28 150.00 1590. 0.79 Sol_RF 1382.04 60.00 179.99 60.00 -164.07 120.00 1571. 0.78 Sol_RF 14 141.01 30.00 179.99 30.00 -77.99 150.00 1554. 0.77 Sol_RF 15 123.63 -155.38 179.98 24.62 112.74 155.38 1517. 0.75 Sol_RF 16 148.80 30.00 179.99 30.00 -62.39 150.00 1450. 0.72 Sol_RF 17 142.61 30.00 180.00 30.00 -74.78 150.00 1439. 0.72 Sol_RF 1872.25 -150.00 179.99 30.00 -144.50 150.00 1422. 0.71 Sol_RF 1947.42 -120.00 179.98 60.00 -94.83 120.00 1417. 0.71 Sol_RF 20 153.12 30.00 179.98 30.00 -53.75 150.00 1292. 0.64 Sol_RF 21 155.99 30.00 179.98 30.00 -48.01 150.00 1274. 0.63 Sol_RF 22 138.05 30.00 179.99 30.00 -83.91 150.00 1258. 0.63 Sol_RF 2354.12 120.00 89.15 60.00 69.320.00 1254. 0.62 Sol_RF 24 129.04 -136.48 179.99 43.52 101.93 136.48 1193. 0.59 Sol_RF 25 138.65 -164.29 179.99 15.71 82.69 164.29 1185. 0.59 Sol_RF 2684.16 51.37 179.98 51.37 -168.32 128.63 1176. 0.59 Sol_RF 2790.00 150.00 59.82 60.00 59.82 -60.00 1162. 0.58 Sol_RF 2843.66 -133.74 179.98 46.26 -87.31 133.74 1161. 0.58 Sol_RF 29 127.85 -169.33 179.99 10.67 104.29 169.33 1153. 0.57 Sol_RF 30 124.15 30.00 179.99 30.00 -111.71 150.00 1147. 0.57 My question is: 1. For a 70 kDa protein compelx, is it common to have such a large cell with a dimention as long as 480 angstrom? 2. Is it possible that the longest dimention of cell is doubled? If it is, how to divide it? 3. How to interpret the self-rotation results. The results from CNS and Molrep differs so much. 4. Any other suggestions on the molecular replacement are appraciated. Thanks. Wei Zhang PKU
[ccp4bb] Van der Waals contacts
Hi CCP4ers Perhaps I am hashing over old news.but We are having a discussion about Van Der Waals contacts and effective contacts i.e. the real distance of a VDW bump between say a CH and a CH group which sometimes is described as between a C and a C as i.e. 2x 1.6A and ending about 4A but not including hydrogen. Some programs list contacts, to say a ligand, as far as 6A apart and some of the simulation programs use that distance too for contacts for protein protein interactions. Does anyone know of a good paper that discusses the effective distance or has a comment on where a VDW force may begin and end or it's effective distance - though some say it never truly ends just approaches zero... G Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Van der Waals contacts
Hello, Van der Waals Forces: A Handbook for Biologists, Chemists, Engineers, and Physicists by V. Adrian Parsegian Give it a try! Artem Hi CCP4ers Perhaps I am hashing over old news.but We are having a discussion about Van Der Waals contacts and effective contacts i.e. the real distance of a VDW bump between say a CH and a CH group which sometimes is described as between a C and a C as i.e. 2x 1.6A and ending about 4A but not including hydrogen. Some programs list contacts, to say a ligand, as far as 6A apart and some of the simulation programs use that distance too for contacts for protein protein interactions. Does anyone know of a good paper that discusses the effective distance or has a comment on where a VDW force may begin and end or it's effective distance - though some say it never truly ends just approaches zero... G Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Active site similarity search
Sorry for asking a non-ccp4 question. Is there any way to mine the PDB to accumulate the structures which have similar binding site(ligand binding pocket) with that of a particular structure. If anyone can suggest a program to do this would be great. I want to do this computationally. You could probably use SPASM for this - see: http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=9917419dataSource=MED (for a reprint: http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=48) If you don't want to install the whole caboodle, you can use Mark Harris' SPASM server - http://eds.bmc.uu.se/eds/spana.php?spasm --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
[ccp4bb] Coot question
Greetings all I am trying to change the color scheme Coot uses when opening PDB files. When I open two seperate PDB files in the same session I would like to change the colors such that there is a clear and distinct difference between the two chains (coot does not always do this), ie red and green instead of Coot offering me green and light green. I am comparing two different maps which are quite similar so the distinction is needed. Any ideas? James
[ccp4bb] Summary IPTG suppliers (mainly Europe)
Current EU IPTG prices in euros, approximate, without tax, delivery or currency exchange fees. Prices are quoted as to my best knowledge, but of course may be different when you order at a different time or from a different place. I do not claim it is complete. Apollo Scientific (UK): 5 g 18 euros, 25 g 85 euros Biosynth (Switzerland): 10 g 40 euros, 25 g 89 euros, 50 g 160 euros, 100 g 286 euros ForMedium (UK): 1 g 9 euros, 5 g 28 euros, 10 g 51 euros, 25 g 118 euros, 100 g 378 euros, 250 g 765 euros Melford (UK): 1 g 10 euros, 5 g 31 euros, 10 g 56 euros, 25 g 131 euros, 50 g 244 euros, 100 g 450 euros Nzytech (Portugal): 1 g 28 euros, 5 g 52 euros Eurogentec (via Cultek): 1 g 21 euros, 5 g 84 euros Qiagen (via Izasa): 5 g 142 euros Promega: 50 g 1140 euros, 5 g 181 euros, 1 g 61 euros Invitrogen: 1 g, 44 euros Sigma-Aldrich: 5 g 250 euros, 10 g 494 euros Fermentas was also mentioned at 33 pounds for 5 g, but their web does not let you see the price unless you register (it also does not mention Spain in the shipping list, perhaps it has a distributor here I am unaware of). It appears UK/Swiss companies are the cheapest, and the UK is in Europe, although some people seem to think otherwise. Seriously, for us ordering the UK is as easy as ordering from Spain or other European countries. I am not sure how easy ordering from Switzerland would be, I have never tried... All people give good refs of the supplier used (i.e. absence of expression problems), except for one person, who only uses Sigma IPTG after problems with other sources. Another supplier mentioned without EU distributors was: Gold BioTechnologies: 25 g 99 USD, 100 g 309 USD, 300g 799 USD Several people mentioned Studiers auto-induction methods, which avoids having to use IPTG and gives them better cell density and, in some cases, more expression of soluble protein. Thanks to all for their comments and knowledge of companies I had never heard of and did not find with Google, Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/
Re: [ccp4bb] European IPTG suppliers
We get most of our 'standard' lab chemicals (IPTG, Tris, etc.) from Melford - http://www.melford.co.uk For IPTG: 1 gm8.00 ₤ 5 gm25.00 ₤ 10 gm 45.00 ₤ 25 gm 105.00 ₤ 50 gm 195.00 ₤ 100 gm 360.00 ₤ Cheers, Stephen 2009/7/13 Mark J. van Raaij mark.vanra...@usc.es: Dear All, as a structural biology lab, we use quite a bit of IPTG...not cheap and needs to be of sufficient quality for bacterial protein expression induction. Therefore I thought it would be useful to compare supplier prices in Euros, realising that of course pricing may vary across different countries and in time. Personally, I am only interesting in EU (Schengen) suppliers, because ordering from outside is too complicated for us. But I will make a compilation of replies and include other ones. Comments about negociable large quantity orders (up to 100 g) are also welcome. Greetings, Mark IPTG prices in Spain, approx. without tax. Qiagen (via Izasa): 5 g 142 euros Promega: 50 g 1140 euros, 5 g 181 euros, 1 g 61 euros Sigma: 10 g 494 euros, 5 g 250 euros Invitrogen: 1 g, 44 euros Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
Re: [ccp4bb] Coot question
You can change the color of any map or molecule to any color you wish by using the Map Colour and Bond Colour menus. After you have opened a map or molecular model simply go to the Edit menu at the top of the window; Map Colour will be the top option and Bond Colour will be the third from the top. Cheers, Jim On Tue, Jul 14, 2009 at 12:50 PM, James Tucker Swindell II jtswi...@secsg.uga.edu wrote: Greetings all I am trying to change the color scheme Coot uses when opening PDB files. When I open two seperate PDB files in the same session I would like to change the colors such that there is a clear and distinct difference between the two chains (coot does not always do this), ie red and green instead of Coot offering me green and light green. I am comparing two different maps which are quite similar so the distinction is needed. Any ideas? James -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
Re: [ccp4bb] Summary IPTG suppliers (mainly Europe)
When there is a greater-than-10-fold range of prices, as here, it seems that there is unfair business going on. I am no expert on European business law, but I suspect there might be something illegal here. Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Mark J. van Raaij mark.vanra...@usc.es To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, July 14, 2009 11:56 AM Subject: [ccp4bb] Summary IPTG suppliers (mainly Europe) Current EU IPTG prices in euros, approximate, without tax, delivery or currency exchange fees. Prices are quoted as to my best knowledge, but of course may be different when you order at a different time or from a different place. I do not claim it is complete. Apollo Scientific (UK): 5 g 18 euros, 25 g 85 euros Biosynth (Switzerland): 10 g 40 euros, 25 g 89 euros, 50 g 160 euros, 100 g 286 euros ForMedium (UK): 1 g 9 euros, 5 g 28 euros, 10 g 51 euros, 25 g 118 euros, 100 g 378 euros, 250 g 765 euros Melford (UK): 1 g 10 euros, 5 g 31 euros, 10 g 56 euros, 25 g 131 euros, 50 g 244 euros, 100 g 450 euros Nzytech (Portugal): 1 g 28 euros, 5 g 52 euros Eurogentec (via Cultek): 1 g 21 euros, 5 g 84 euros Qiagen (via Izasa): 5 g 142 euros Promega: 50 g 1140 euros, 5 g 181 euros, 1 g 61 euros Invitrogen: 1 g, 44 euros Sigma-Aldrich: 5 g 250 euros, 10 g 494 euros Fermentas was also mentioned at 33 pounds for 5 g, but their web does not let you see the price unless you register (it also does not mention Spain in the shipping list, perhaps it has a distributor here I am unaware of). It appears UK/Swiss companies are the cheapest, and the UK is in Europe, although some people seem to think otherwise. Seriously, for us ordering the UK is as easy as ordering from Spain or other European countries. I am not sure how easy ordering from Switzerland would be, I have never tried... All people give good refs of the supplier used (i.e. absence of expression problems), except for one person, who only uses Sigma IPTG after problems with other sources. Another supplier mentioned without EU distributors was: Gold BioTechnologies: 25 g 99 USD, 100 g 309 USD, 300g 799 USD Several people mentioned Studiers auto-induction methods, which avoids having to use IPTG and gives them better cell density and, in some cases, more expression of soluble protein. Thanks to all for their comments and knowledge of companies I had never heard of and did not find with Google, Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/
Re: [ccp4bb] moelcular replacement with large cell
Are you sure you're using the right space group? For example, what does phenix.xtriage suggest for your space group? Ho Confometrx
[ccp4bb] Protein Sequence Analysis Software
Dear all, I'm sorry for the somewhat non-ccp4 related questions, but here goes; 1. Could anyone recommend a good mailing list for bioinformatics related problems, where I might be able to re-ask question 2. 2. Does anyone know of some good software for visualization of the domain analysis of the primary sequence of a protein? What I would like to do is search a protein sequence, or most preferably, a multiple alignment of protein sequences for conserved domains against the pfam database, and then visualize the results. Preferably, I would like a output to be in a vector format. Thanks! and all the best, --Buz
Re: [ccp4bb] moelcular replacement with large cell
Dears, I am sorry for not saying it clearly. By looking at the 00l lines and by Phenix.xtrige, it is probable P6122 or P6522. In the molecular replacement searching, I have set to search all the possible of space group of P622 in Phaser and Molrep. But all the trials failed. My model is the structure large subunit of the complex. So the sequence identity is 100%. The large subunit is composed by two domains. So in the search, I divided the model into two parts. Any other suggestions? Thanks and best wishes. On Tue, Jul 14, 2009 at 8:11 PM, Randy Read rj...@cam.ac.uk wrote: Hi, You didn't say whether you are absolutely certain that it is P622 (i.e. you have measured complete data for all the h00, 0k0 and 00l lines and found no systematic absences) or whether it could be another space group with the same Laue symmetry. Unless you're absolutely certain, then you have to try all possible choices of space group. In fact, I'd be surprised to see such a long c cell edge if there is no screw axis, but unsurprised if it were (say) a 6(1) screw axis. The other thing you didn't mention is how good you expect your models to be. How high is the sequence identity between the model and the target for each component? Could there be flexibility in the molecules? Good luck! Randy Read On 14 Jul 2009, at 12:23, Wei Zhang wrote: Dears, I am doing molecular replacement of a protein complex with a P622 data set with large cell parameters (a=b=135, c=480). The data set seems well. R merge is 0.17 for all and 0.70 for the last shell of 2.9 angstrom. I am not sure it is a complex in the crystal. Phenix analysis reveal there is no twin. The proposed protein complex is about 70 kDa with a larger subunit of 50 kDa and a small subunit of 20 kDa. The matthews analysis indicates that there might be 3 complexes in the ASU. The structure of the 50 kDa subunit is known while the 20 kDa one is unknown. But molecular replacement failed with either Phaser or Molrep. Self-rotation with CNS reported the result as below: ! index, psi, phi, kappa, RF-function ( 0.25) 1 0.000 0.000 180.000 29.7217 Self-ratation with Molrep reported the result as below: Number of RF peaks : 30 thetaphi chialphabeta gamma Rf Rf/sigma Sol_RF 1 0.000.000.000.000.000.000.3444E+05 17.13 Sol_RF 290.00 -80.07 179.990.00 180.00 -19.86 5061. 2.52 Sol_RF 390.00 -65.53 179.990.00 180.00 -48.94 4890. 2.43 Sol_RF 490.00 -76.12 179.990.00 180.00 -27.76 4722. 2.35 Sol_RF 511.42 90.00 61.00 30.00 11.53 30.00 2438. 1.21 Sol_RF 6 164.38 60.00 179.99 60.00 -31.24 120.00 1850. 0.92 Sol_RF 785.13 -141.54 179.97 38.32 -170.26 141.40 1805. 0.90 Sol_RF 890.00 -60.00 90.00 30.00 -90.00 -30.00 1764. 0.88 Sol_RF 984.07 -144.87 179.96 34.98 -168.15 144.73 1743. 0.87 Sol_RF 1072.25 -60.00 89.30 46.76 -84.03 -13.24 1665. 0.83 Sol_RF 11 138.24 -130.77 180.00 49.23 83.52 130.77 1608. 0.80 Sol_RF 12 170.36 30.00 179.99 30.00 -19.28 150.00 1590. 0.79 Sol_RF 1382.04 60.00 179.99 60.00 -164.07 120.00 1571. 0.78 Sol_RF 14 141.01 30.00 179.99 30.00 -77.99 150.00 1554. 0.77 Sol_RF 15 123.63 -155.38 179.98 24.62 112.74 155.38 1517. 0.75 Sol_RF 16 148.80 30.00 179.99 30.00 -62.39 150.00 1450. 0.72 Sol_RF 17 142.61 30.00 180.00 30.00 -74.78 150.00 1439. 0.72 Sol_RF 1872.25 -150.00 179.99 30.00 -144.50 150.00 1422. 0.71 Sol_RF 1947.42 -120.00 179.98 60.00 -94.83 120.00 1417. 0.71 Sol_RF 20 153.12 30.00 179.98 30.00 -53.75 150.00 1292. 0.64 Sol_RF 21 155.99 30.00 179.98 30.00 -48.01 150.00 1274. 0.63 Sol_RF 22 138.05 30.00 179.99 30.00 -83.91 150.00 1258. 0.63 Sol_RF 2354.12 120.00 89.15 60.00 69.320.00 1254. 0.62 Sol_RF 24 129.04 -136.48 179.99 43.52 101.93 136.48 1193. 0.59 Sol_RF 25 138.65 -164.29 179.99 15.71 82.69 164.29 1185. 0.59 Sol_RF 2684.16 51.37 179.98 51.37 -168.32 128.63 1176. 0.59 Sol_RF 2790.00 150.00 59.82 60.00 59.82 -60.00 1162. 0.58 Sol_RF 2843.66 -133.74 179.98 46.26 -87.31 133.74 1161. 0.58 Sol_RF 29 127.85 -169.33 179.99 10.67 104.29 169.33 1153. 0.57 Sol_RF 30 124.15 30.00 179.99 30.00 -111.71 150.00 1147. 0.57 My question is: 1. For a 70 kDa protein compelx, is it common to have such a large cell with a dimention as long as 480 angstrom? 2. Is it possible that the longest dimention of cell is doubled? If it is, how to divide it? 3. How to interpret the self-rotation results. The results from CNS and Molrep
[ccp4bb] The intensity of low resolution
Dear all: A small mutant protein (~7KDa) was deffracted to ~3.5A. All staticstis data looked good. The Intesity in low resolution seems a little bit weak. I tried to run the molecular replacement, but there was no significant result.Will it influence the phasing ? Any help would appreciated. Best wish, jaishin Shell Lower Upper Average Average Norm. Linear Square limitAngstrom I error stat Chi**2 R-fac R-fac 30.00 7.50 602.718.015.3 1.090 0.069 0.057 7.50 5.97 312.619.718.6 0.964 0.148 0.131 5.97 5.22 263.722.921.8 0.968 0.198 0.162 5.22 4.75 340.526.224.8 1.062 0.185 0.161 4.75 4.41 383.728.526.9 1.129 0.188 0.172 4.41 4.15 311.429.828.2 1.139 0.243 0.226 4.15 3.94 227.130.728.9 1.008 0.332 0.298 3.94 3.77 173.231.430.0 1.039 0.444 0.399 3.77 3.62 150.733.331.3 1.041 0.507 0.453 3.62 3.50 118.834.031.7 0.979 0.659 0.581 All reflections289.627.425.7 1.042 0.228 0.179
Re: [ccp4bb] moelcular replacement with large cell
Hello dear Wei, 1) Your dataset has a high overall Rmerge. The outmost shell (70%) is very high, which suggests a need to shrink resolution. What about I/ s(I), redundancy and completeness? Also, how many reflections (percentage) have been subjected to rejection? Too many rejections may mean a SG error. 2) Software analyses including Phenix.xtriage give good suggestions, but they should be used reasonably. P6n22 could be twinned from P6n or P3n12 or P3n21 or even P3n, when close to be perfectly twinned. 3) Please try a little more analyses of the cell shape and A.U. shape (very long in your case), with Matthews' coefficient analyses, you may get more hints about packing and SG. 4) Try to find one molecule first in such a big A.U. [Automatic scripts have a higher chance to fail than a smart manual scrip (very personal)]. 5) Use a lower resolution ~4-5 Å data to do a better self rotation function. Why do not paste a .ps plot for the SR peaks. Good luck. Lijun On Jul 14, 2009, at 4:23 AM, Wei Zhang wrote: Dears, I am doing molecular replacement of a protein complex with a P622 data set with large cell parameters (a=b=135, c=480). The data set seems well. R merge is 0.17 for all and 0.70 for the last shell of 2.9 angstrom. I am not sure it is a complex in the crystal. Phenix analysis reveal there is no twin. The proposed protein complex is about 70 kDa with a larger subunit of 50 kDa and a small subunit of 20 kDa. The matthews analysis indicates that there might be 3 complexes in the ASU. The structure of the 50 kDa subunit is known while the 20 kDa one is unknown. But molecular replacement failed with either Phaser or Molrep. Self-rotation with CNS reported the result as below: ! index, psi, phi, kappa, RF-function ( 0.25) 1 0.000 0.000 180.000 29.7217 Self-ratation with Molrep reported the result as below: Number of RF peaks : 30 thetaphi chialphabeta gamma RfRf/sigma Sol_RF 1 0.000.000.000.000.000.00 0.3444E+05 17.13 Sol_RF 290.00 -80.07 179.990.00 180.00 -19.86 5061. 2.52 Sol_RF 390.00 -65.53 179.990.00 180.00 -48.94 4890. 2.43 Sol_RF 490.00 -76.12 179.990.00 180.00 -27.76 4722. 2.35 Sol_RF 511.42 90.00 61.00 30.00 11.53 30.00 2438. 1.21 Sol_RF 6 164.38 60.00 179.99 60.00 -31.24 120.00 1850. 0.92 Sol_RF 785.13 -141.54 179.97 38.32 -170.26 141.40 1805. 0.90 Sol_RF 890.00 -60.00 90.00 30.00 -90.00 -30.00 1764. 0.88 Sol_RF 984.07 -144.87 179.96 34.98 -168.15 144.73 1743. 0.87 Sol_RF 1072.25 -60.00 89.30 46.76 -84.03 -13.24 1665. 0.83 Sol_RF 11 138.24 -130.77 180.00 49.23 83.52 130.77 1608. 0.80 Sol_RF 12 170.36 30.00 179.99 30.00 -19.28 150.00 1590. 0.79 Sol_RF 1382.04 60.00 179.99 60.00 -164.07 120.00 1571. 0.78 Sol_RF 14 141.01 30.00 179.99 30.00 -77.99 150.00 1554. 0.77 Sol_RF 15 123.63 -155.38 179.98 24.62 112.74 155.38 1517. 0.75 Sol_RF 16 148.80 30.00 179.99 30.00 -62.39 150.00 1450. 0.72 Sol_RF 17 142.61 30.00 180.00 30.00 -74.78 150.00 1439. 0.72 Sol_RF 1872.25 -150.00 179.99 30.00 -144.50 150.00 1422. 0.71 Sol_RF 1947.42 -120.00 179.98 60.00 -94.83 120.00 1417. 0.71 Sol_RF 20 153.12 30.00 179.98 30.00 -53.75 150.00 1292. 0.64 Sol_RF 21 155.99 30.00 179.98 30.00 -48.01 150.00 1274. 0.63 Sol_RF 22 138.05 30.00 179.99 30.00 -83.91 150.00 1258. 0.63 Sol_RF 2354.12 120.00 89.15 60.00 69.320.00 1254. 0.62 Sol_RF 24 129.04 -136.48 179.99 43.52 101.93 136.48 1193. 0.59 Sol_RF 25 138.65 -164.29 179.99 15.71 82.69 164.29 1185. 0.59 Sol_RF 2684.16 51.37 179.98 51.37 -168.32 128.63 1176. 0.59 Sol_RF 2790.00 150.00 59.82 60.00 59.82 -60.00 1162. 0.58 Sol_RF 2843.66 -133.74 179.98 46.26 -87.31 133.74 1161. 0.58 Sol_RF 29 127.85 -169.33 179.99 10.67 104.29 169.33 1153. 0.57 Sol_RF 30 124.15 30.00 179.99 30.00 -111.71 150.00 1147. 0.57 My question is: 1. For a 70 kDa protein compelx, is it common to have such a large cell with a dimention as long as 480 angstrom? 2. Is it possible that the longest dimention of cell is doubled? If it is, how to divide it? 3. How to interpret the self-rotation results. The results from CNS and Molrep differs so much. 4. Any other suggestions on the molecular replacement are appraciated. Thanks. Wei Zhang PKU Lijun Liu, PhD Institute of Molecular Biology Department of
