Re: [ccp4bb] Professor Dame Louise Johnson
A very nice picture of Prof. Louise Johnson can be found on http://www.flickr.com/photos/wellcomeimages/5814718414/ The picture was taken at Diamond's IO2 beam line. Condolences to her family and friends. Fred.
Re: [ccp4bb] ideal rms bond length
Hi there, acceptable deviations from ideal geometry depends on the resolution of the data set. There are several papers dealing with this, including the paper describing the tool used in Phenix. I couldn't find the resolution of the data set used during refinement in your mail so it is difficult to compare the data given to that expected for a well refined structure at that resolution. Fred. PS the figures shown do not seem to be totally unreasonable. The r.m.s. deviations concerning the angles could be improved though IMHO - again not knowing the resolution of the data set On 02/10/12 23:49, Faisal Tarique wrote: Dear all i request you to please answer my basic query about the ideal acceptable rmsbond length obtained during refmac refinement..is the data acceptable in mine case which is as follows.. NcycRfactRfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2090 0.2079 0.875226315. 11985.5 0.0278 1.389 2.718 1.261 0.198 1 0.2064 0.2284 0.850226313. 12201.1 0.0285 1.427 2.733 1.271 0.204 2 0.2076 0.2373 0.837226944. 12289.9 0.0248 1.242 2.598 1.200 0.187 3 0.2092 0.2429 0.828227495. 12341.7 0.0222 1.107 2.458 1.128 0.173 4 0.2100 0.2468 0.822227753. 12372.4 0.0211 1.053 2.377 1.086 0.166 5 0.2104 0.2500 0.818227942. 12395.7 0.0204 1.021 2.326 1.061 0.161 6 0.2108 0.2522 0.814228075. 12411.5 0.0200 0.999 2.289 1.042 0.158 7 0.2111 0.2537 0.812228162. 12421.8 0.0197 0.984 2.265 1.030 0.156 8 0.2113 0.2550 0.810228228. 12430.5 0.0194 0.971 2.243 1.020 0.154 9 0.2114 0.2559 0.809228300. 12436.1 0.0192 0.962 2.228 1.012 0.153 10 0.2116 0.2568 0.808228348. 12441.7 0.0191 0.957 2.218 1.008 0.152 11 0.2118 0.2574 0.807228394. 12446.2 0.0190 0.951 2.210 1.004 0.151 12 0.2119 0.2581 0.806228421. 12449.6 0.0189 0.948 2.203 1.001 0.151 13 0.2119 0.2585 0.805228440. 12452.7 0.0189 0.944 2.198 0.998 0.150 14 0.2120 0.2590 0.805228461. 12455.0 0.0188 0.941 2.194 0.996 0.150 15 0.2121 0.2593 0.804228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] ideal rms bond length
Thanx everybody for your nice suggestions.. On Wed, Oct 3, 2012 at 3:19 AM, Faisal Tarique faisaltari...@gmail.comwrote: Dear all i request you to please answer my basic query about the ideal acceptable rmsbond length obtained during refmac refinement..is the data acceptable in mine case which is as follows.. NcycRfactRfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2090 0.2079 0.875226315. 11985.5 0.0278 1.389 2.718 1.261 0.198 1 0.2064 0.2284 0.850226313. 12201.1 0.0285 1.427 2.733 1.271 0.204 2 0.2076 0.2373 0.837226944. 12289.9 0.0248 1.242 2.598 1.200 0.187 3 0.2092 0.2429 0.828227495. 12341.7 0.0222 1.107 2.458 1.128 0.173 4 0.2100 0.2468 0.822227753. 12372.4 0.0211 1.053 2.377 1.086 0.166 5 0.2104 0.2500 0.818227942. 12395.7 0.0204 1.021 2.326 1.061 0.161 6 0.2108 0.2522 0.814228075. 12411.5 0.0200 0.999 2.289 1.042 0.158 7 0.2111 0.2537 0.812228162. 12421.8 0.0197 0.984 2.265 1.030 0.156 8 0.2113 0.2550 0.810228228. 12430.5 0.0194 0.971 2.243 1.020 0.154 9 0.2114 0.2559 0.809228300. 12436.1 0.0192 0.962 2.228 1.012 0.153 10 0.2116 0.2568 0.808228348. 12441.7 0.0191 0.957 2.218 1.008 0.152 11 0.2118 0.2574 0.807228394. 12446.2 0.0190 0.951 2.210 1.004 0.151 12 0.2119 0.2581 0.806228421. 12449.6 0.0189 0.948 2.203 1.001 0.151 13 0.2119 0.2585 0.805228440. 12452.7 0.0189 0.944 2.198 0.998 0.150 14 0.2120 0.2590 0.805228461. 12455.0 0.0188 0.941 2.194 0.996 0.150 15 0.2121 0.2593 0.804228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] ideal rms bond length
Dear Faisal - There are a few problems with your refinement. First and foremost, your R factors increase instead of decreasing! This is associated with a decrease in geometry rmsd, suggesting that Refmac is trying to fix an incorrect model using an excessively tight geometry weight. Second, your geometry rmsd values are still quite high. You don't say what resolution you have to work with, but given your R factors, I would expect you have something in the 2 to 2.5 A range. Your rmsBOND values would typically be below 0.015 at this resolution. It's possible you have a few areas of your model with very bad geometry which are raising the global values even though everything else is mostly OK. Third, I wonder why your R and Rfree are so close at the start of refinement. The low R values suggest a late-stage refined model, not an initial molecular replacement solution or something similar. If you're starting with an isomorphous structure, you need to use the same free R set as was used in the previous refinement in order to keep your R free set uncontaminated. You should examine your model carefully and look for regions that don't have strong electron density to support them. Also look for bad geometry: bond and angle deviations greater than 5 sigma (these will be in the Refmac log file), bad rotamers, bad Ramachandran position, etc. Regions which are of poor quality should be removed from the model and rebuilt into unbiased density in later refinement rounds. (Or if the electron density stays poor, leave the region out of the model.) Good luck, Matt On 10/2/12 5:49 PM, Faisal Tarique wrote: Dear all i request you to please answer my basic query about the ideal acceptable rmsbond length obtained during refmac refinement..is the data acceptable in mine case which is as follows.. NcycRfactRfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2090 0.2079 0.875226315. 11985.5 0.0278 1.389 2.718 1.261 0.198 1 0.2064 0.2284 0.850226313. 12201.1 0.0285 1.427 2.733 1.271 0.204 2 0.2076 0.2373 0.837226944. 12289.9 0.0248 1.242 2.598 1.200 0.187 3 0.2092 0.2429 0.828227495. 12341.7 0.0222 1.107 2.458 1.128 0.173 4 0.2100 0.2468 0.822227753. 12372.4 0.0211 1.053 2.377 1.086 0.166 5 0.2104 0.2500 0.818227942. 12395.7 0.0204 1.021 2.326 1.061 0.161 6 0.2108 0.2522 0.814228075. 12411.5 0.0200 0.999 2.289 1.042 0.158 7 0.2111 0.2537 0.812228162. 12421.8 0.0197 0.984 2.265 1.030 0.156 8 0.2113 0.2550 0.810228228. 12430.5 0.0194 0.971 2.243 1.020 0.154 9 0.2114 0.2559 0.809228300. 12436.1 0.0192 0.962 2.228 1.012 0.153 10 0.2116 0.2568 0.808228348. 12441.7 0.0191 0.957 2.218 1.008 0.152 11 0.2118 0.2574 0.807228394. 12446.2 0.0190 0.951 2.210 1.004 0.151 12 0.2119 0.2581 0.806228421. 12449.6 0.0189 0.948 2.203 1.001 0.151 13 0.2119 0.2585 0.805228440. 12452.7 0.0189 0.944 2.198 0.998 0.150 14 0.2120 0.2590 0.805228461. 12455.0 0.0188 0.941 2.194 0.996 0.150 15 0.2121 0.2593 0.804228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] Professor Dame Louise Johnson
Professor Dame Louise Johnson was my thesis supervisor and I am saddened by her departure. I would like to encourage the crystallographic community to contribute to: http://en.wikipedia.org/wiki/Louise_Johnson so that her achievemens can be remenbered and can continue to inspire future generations of crystallographers. Those that have access to a copyright -free photograph can upload it to Wikipedia Commons: http://commons.wikimedia.org/wiki/Main_Page I would like to extend my condolences her family and all her friends. Enrico. -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
[ccp4bb] NIH postdoctoral position in membrane protein crystallography
A postdoctoral position is available for structural and functional analysis of proteins involved in virulence and/or survival in pathogenic bacteria. We are particularly interested in developing drugs and vaccines that target multidrug resistant bacterial strains. See recent examples of our work in/Nature/483:53-58 (2012) http://www.nature.com/nature/journal/v483/n7387/full/nature10823.htmland/Proc. Natl. Acad. Sci. USA/109:9857-9862 (2012) http://www.pnas.org/content/109/25/9857.long. Candidates must have experience in protein structure determination by X-ray crystallography and will ideally have some experience in membrane or soluble protein expression, purification, and crystallization. Good biochemistry skills are essential. We are part of an interactive group of structural biologists sharing common home source X-ray facilities, dedicated access to beamlines at APS, and a common weekly group meeting. Applicants must have a PhD and less than five years of postdoctoral experience. Please send CV, including the names and addresses of three references, to Susan Buchanan Laboratory of Molecular Biology NIDDK Building 50, Room 4503 50 South Drive Bethesda, MD 20892-8030 e-mailskbuc...@helix.nih.gov mailto:skbuc...@helix.nih.gov -- Susan Buchanan Laboratory of Molecular Biology NIDDK, NIH 50 South Drive, Room 4503 Bethesda, MD 20892-8030 Phone (+1) 301-594-9222 Fax (+1) 301-480-0597 Web: http://www-mslmb.niddk.nih.gov/buchanan/index.html
[ccp4bb] off topic: reproducing hits from organic solvents
Hi all, I recently got some hits from a Mosquito grown at 18C with PEG4000 and 10% propanol. I've tried reproducing these hits using the standard 24 well format with no success, even with playing with PEG and propanol concentrations. The initial screening solution was from a kit that's been sitting in the cold room for the better part of 2 years. Does anyone here have any tips or tricks in reproducing crystals grown from organic solvents? Many thanks in advance, Peter
Re: [ccp4bb] off topic: reproducing hits from organic solvents
Peter We make a 96-well plate that was originally made for microbatch-under-oil, which has a large moat or well around the whole plate. My old friend Lesley Haire had a lot of success with this plate for a condition that contained isopropanol. She set up the drops without isoprop, covered them with Al's Oils (silicone mixed with paraffin oil from Hampton Research), then put water containing the appropriate concentration of isoprop in the moat (in her case 10 - 20%). THe isoprop diffused through the oil and into the drops. Since the oil is also saturated with isoprop it makes a very good barrier and stops the isoprop from evaporating from the drops when you harvest your crystals. As Lesley pointed out you can even set up a random screen without isopropanol, then diffuse the isopropanol in afterwards. Let me know if you - or anyone else - would like some samples of the plate. Unfortunately it won't fit on a Mosquito, but you can use it by hand, see ref below. Regarding your question below, bear in mind that water and oil can both go through plastic tubes (slowly). I hope it works for you Patrick Refs and info: See http://www.douglas.co.uk/winner1.htm http://www.douglas.co.uk/vb.htm *Nature* *431* (2004), pp 481-485. On 3 October 2012 17:37, Peter Hsu hsuu...@u.washington.edu wrote: Hi all, I recently got some hits from a Mosquito grown at 18C with PEG4000 and 10% propanol. I've tried reproducing these hits using the standard 24 well format with no success, even with playing with PEG and propanol concentrations. The initial screening solution was from a kit that's been sitting in the cold room for the better part of 2 years. Does anyone here have any tips or tricks in reproducing crystals grown from organic solvents? Many thanks in advance, Peter -- 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
Re: [ccp4bb] off topic: reproducing hits from organic solvents
Doesn't seem like there'd have been much isopropanol left in that tube after 2 years. In fact, your PEG may have gone off as well, changing the pH and god knows what else. Try screening pH and leaving out isopropanol in your optimization. phx On 3 October 2012 17:37, Peter Hsu hsuu...@u.washington.edu mailto:hsuu...@u.washington.edu wrote: Hi all, I recently got some hits from a Mosquito grown at 18C with PEG4000 and 10% propanol. I've tried reproducing these hits using the standard 24 well format with no success, even with playing with PEG and propanol concentrations. The initial screening solution was from a kit that's been sitting in the cold room for the better part of 2 years. Does anyone here have any tips or tricks in reproducing crystals grown from organic solvents? Many thanks in advance, Peter -- patr...@douglas.co.uk mailto: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
