Re: [ccp4bb] MAD and twinning
So one obvious questions: was your crystal fully bathed in the beam ? If not: would be interesting to try having a look at the unmerged data...Well, easier to suggest than to do... I recall being frowned upon by my former supervisor (a small molecule crystallographer) for having crystals larger than the beam and for looking at fishnets In any case, xtriage will detwin data with anomalous signal properly. download the latest version from www.phenix-online.org (either cci_apps or the latest phenix development release) Note that according to Dauter (sorry, i forgot the reference), finding a substructure in twinned data is usually not a problem (given reasonable data). Improvement on the density modification according to Dauter can be obtained by performing density modification on detwinned data. HTH Peter
Re: [ccp4bb] Solving a structure by MR with a pseudo-translation vector
Dear Prof. Fan, I do not think that this is a neccesarely an incommensurable structure. A lot of structures have translational NCS close to a translational that would make the space group higher and/or the primitive cell smaller. If one has C2221 and one destroys the centring operation x,y+1/2,z+1/2 by introducing a small perturbation, one just has pseudo symmetry/pseudo centring. If the data is processed in P212121, there need not be satelite reflections. If one wrongly assumes the sg to be C2221, there are 'satelite' reflections: the systematic absences due to the imperfect lattice translation (x,y+1/2,z+1/2). HTH Peter It seems to me that you are solving an incommensurately modulated structure,since the pseudo-translation vector t = 0a + 0.47b + 0.5c having the b component equal to 0.47 and not exactly 0.5. There should be satellite reflections which are NOT on nodes of the reciprocal lattice you have chosen. If you try to solve an incommensurately modulated structure by rejecting satellites, what you get will be the “averaged structure” and not the true structure. In this case R factors should considerably higherthan that of normal cases. More details about solving incommensuratelymodulated structures can be found on the Webpage: http://cryst.iphy.ac.cn http://cryst.iphy.ac.cn/ Hai-fu -- Professor Fan, Hai-fu Institute of Physics Chinese Academy of Sciences Beijing 100080, P.R. China Email: [EMAIL PROTECTED] URL: http://cryst.iphy.ac.cn http://cryst.iphy.ac.cn/ -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Peter J Stogios Sent: 2007年3月25日 4:52 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solving a structure by MR with a pseudo- translation vector Hello, I posted a message about this a month ago and thanks to everyone for their responses. At the time, I did not fully appreciate the problem I was dealing with so this time my question is much more specific. I would very much appreciate your help as this structure is turning out to be very difficult to solve! I am trying to solve a structure by MR that should be easy, given that I have solved multiple structures of homologous proteins by the same means. This crystal is 2.6 angstrom, apparently P212121, with two molecules in the asymmetric unit that are related by the pseudo- translation vector (0, 0.47, 0.5). This vector was identified from the Patterson map, it is a peak 45% the height of the origin peak. As well, I have looked at all the reflection parity groups. Based on I/sigmaI values output by Truncate, the k+l = 2n reflections are as high as 2-fold greater in I/sigI vs. k+l = 2n+1 reflections from 16 to 5.1 angstrom. From 5.1 to 2.9 angstrom, the reverse is true: the k +l = 2n reflections are as high as 0.62-fold LOWER in I/sigI vs. k+l = 2n+1. Then, from 2.9 to 2.6 angstrom, each reflection class is approximately equal in intensity. MR using Molrep's multi-copy search, using all reflections, consistently reproduces the pseudo-translation vector as the dyad vector between the two molecules. However, these solutions are not easily noticeable (Molrep just picks the highest score but this score does not stick out from the pack), and these solutions do not refine well via rigid body or restrained refinement in Refmac. I have found some papers that show successful structure determinations by MR with pseudo-translation, but I am not sure which approach to take to solve my structure. Do I need to remove the pseudo-weak or pseudo-strong reflections? Or do I actually use the pseudo-weak or pseudo-strong reflections for the MR since they will contain the information from the pseudo-translation? Which reflections should I refine against? Should I reindex to C222 to reflect the pseudo-face centering from the (0, 0.47, 0.5) vector? Or am I missing something completely? Any help would be very very much appreciated Thanks! Peter ~ Peter J Stogios Ph.D. candidate, Privé Lab Dept. of Medical Biophysics, University of Toronto Toronto Medical Discoveries Tower (TMDT) at MaRS 101 College St., Rm. 4-308 Toronto, Ontario M5G 1L7 e: [EMAIL PROTECTED] w: http://xtal.uhnres.utoronto.ca/prive p: (416) 581-7543
Re: [ccp4bb] Highest shell standards
I typically process my data to a maximum I/sig near 1, and completeness in the highest resolution shell to 50% or greater. It What about maps computed of very incomplete datasets at high resolution? Don't you get a false sense of details when the missing reflections are filled in with DFc when computing a 2MFo-DFc map? P
Re: [ccp4bb] modelling with sad/mad data
Hi Peng Zhang, The presence of radiation damage might cause some problems. Do so see any obvious features in the difference map? Another problem (although I doubt it would cause such a big difference) might be the fact that f' andf f prime are incorrect. Try and refine them (CNS or phenix.refine) maybe. Does your native data have the same free set as the peak data? if not, you are in trouble and have to start from scratch with your native data to be able to make a fair comparison. The 22/25 for 2.7 A seems awfully close together. procheck has not very up to date standards of what is good and what is not. Better use molprobity, available from: http://molprobity.biochem.duke.edu/ HTH Peter - Original Message - From: Peng Zhang [EMAIL PROTECTED] Date: Tuesday, March 20, 2007 6:04 pm Subject: Re: [ccp4bb] modelling with sad/mad data To: CCP4BB@JISCMAIL.AC.UK Maybe I did not make the questions clear, which leading to the misleadings.Firstly, I have collected the mad data and get the phase at synchrotron, the phased Se is quite good for modelling, and get over 70% of the molecule run with resolve autobuilding.The density seems also good for building. But when finally refining the model, the gap between the R(0.22)and free_R(0.32 )is big, even though modelled the Se- methionine. Before collecting the mad data at synchrotron, I already have another native data set collected at home diffractometer (rigku, with R-axis IV++). To my surprise, when I using the same model(first model) and run with this data set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and further refine to R=0.22 and Free_R=0.25), and I got the final model.Thegeometry of the first model and final model(actually no big difference of the two models)is quite good with procheck.The omit map says good enoughwith both of the two models. So I wondering what happened with the peak data? Did the anomolous signalhave much effect on the data? and anyone have the similar experience? First it is always best to refine your model against the highest resolution good quality data that you have available. There was correspondence about the geometric weighting - could you have weighted the Xray data too high and have bad geometry - see previous Emails! And the Free R seems rather low for the Se data. Did you transfer the same Free R set from the native to the Se data? Eleanor Peng Zhang wrote: Dear friends, Recently, I have solved a structure using mad method. When using the peak data(2.3A) as the native for structure refinement, the gap between R factor and R free is big, about 0.1(0.22 and 0.32). I modelled the selenomethionine but the gap still exists. When I changed the data for a real native one(2.7A),it seems OK with R=0.24 and Rf=0.28. Does anyone have the similar experience? what should I pay attention to when using the sad/mad data as the native one for modelling and refinement? Thanks in advance. -- Peng Zhang, Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 20031 P.R. China Tel: 021-5492-1117 Fax: 021-5492-1116 Email: [EMAIL PROTECTED]
Re: [ccp4bb] process SeMet labelled data
Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Properly
Re: [ccp4bb] Multi-copies in one assymetric unit
This isnt any real help but I cant solve a ferritin structure in SG I432 - it probably forms a cage like the other feritins around the origin, but every solution I get clashes with others.. After listening to a lecture by a small molecule crystallographer I wondered whether there isnt some crystal defect but I am not sure how to monitor it.. Eleanor Hi Elenaor, Your problem reminds me of this paper: http://journals.iucr.org/a/issues/2004/04/00/lc0065/index.html Not sure if it is related (probably not), but the phenomenon itself is interesting Cheers Peter
