[ccp4bb] Beamtime at SLS X06SA
= SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE UNDULATOR BEAMLINE X06SA AT SLS FROM MAY - AUGUST 2007 = - PILATUS 6M pixel detector will become available for user operation in May 2007 at the High Resolution Diffractometer; http://pilatus.web.psi.ch/ - Detector upgrade to mar225 CCD on Micro-Diffractometer MD2. This MAD-compatible diffractometer allows for data collection with a beam size of 15 x 5 micrometers. - A robotic sample changer is currently in the commissioning phase and will be available on the Micro-Diffractometer. - SLS is able to provide support for travel and accomodation for two users per trip: http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html - For recent highlights: http://sls.web.psi.ch/view.php/beamlines/px/research/index.html PROPOSAL SUBMISSION DEADLINE: Wednesday, February 15th 2007. For further information and / or proposal submission: http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html Looking forward to seeing you at SLS, Clemens Schulze-Briese -- Dr. Clemens Schulze-Briese - [EMAIL PROTECTED] --- Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone +41 56 310 4533 - Fax -5292 - Secretary -3178
[ccp4bb] Structure reconstruction from NMR constraints?
Hi, What software is recommended for building structures from NMR data? Cheers, Dan.
Re: [ccp4bb] Multi-copies in one assymetric unit
Sometimes this sort of disorder is due to an error , so the first thing is to check very carefully that the solution makes sense. Why are you so sure there are 6 copies in the asymmetric unit? In situations like this I first worry about SG. Is there a pseudo-translation vector? This can make it hard to decide on the SG.. Is there an alternate spacegroup with fewer molecules in the asymm unit? What does the self rotation show? Yanming Zhang wrote: Dear All, Maybe this is a trivial question: My data should have 6 molecules in one assymetric unit. MR could find out 4 molecules. After this, no matter how hard I have tried, no more molecules can be found. At this stage, I suppose that all other copies are dis-ordered. And go ahead to do refinement with 4 molecules (ABCD) available. The density for A is quite good. But for BCD are very dis-ordered. Many breaks in chains. I'd like to ask you: In a situation like this, should I: A, Use NCS for all copies? B Do not use NCS at all? C, Use NCS just for BCD? (even dis-ordered, but similar)? What is the trick to lower down Rfree as soon as possible, if you have experienced the same situation before? Thanks Yanming
Re: [ccp4bb] Multi-copies in one assymetric unit
Assuming that the MR solution is correct (I agree with Eleanor, that you need to be certain about your selection of space group), then use your complete model of chain A superimposed on chains B, C, and D. Then refine and build the heck out of it. In a similar situation, it was relatively easy for me to find two out of three molecules by MR. We were never really convinced that there was a third (Matthews coefficient dicey, suggesting either 2 or 3). After substantial refinement and building, the third chain was apparent, and we rebuilt it completely. Looking at the average B-factors of each chain, and the overall packing environment, chain A was tight, chain B looser, and chain C will substantially fewer contacts. Bernie Santarsiero On Tue, February 13, 2007 10:07 am, Eleanor Dodson wrote: Sometimes this sort of disorder is due to an error , so the first thing is to check very carefully that the solution makes sense. Why are you so sure there are 6 copies in the asymmetric unit? In situations like this I first worry about SG. Is there a pseudo-translation vector? This can make it hard to decide on the SG.. Is there an alternate spacegroup with fewer molecules in the asymm unit? What does the self rotation show? Yanming Zhang wrote: Dear All, Maybe this is a trivial question: My data should have 6 molecules in one assymetric unit. MR could find out 4 molecules. After this, no matter how hard I have tried, no more molecules can be found. At this stage, I suppose that all other copies are dis-ordered. And go ahead to do refinement with 4 molecules (ABCD) available. The density for A is quite good. But for BCD are very dis-ordered. Many breaks in chains. I'd like to ask you: In a situation like this, should I: A, Use NCS for all copies? B Do not use NCS at all? C, Use NCS just for BCD? (even dis-ordered, but similar)? What is the trick to lower down Rfree as soon as possible, if you have experienced the same situation before? Thanks Yanming
Re: [ccp4bb] Structure reconstruction from NMR constraints?
software is recommended for building structures Actually, I can recommend some HARDWARE: It is called 'X-ray diffractometer'. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Dan Bolser Sent: Tuesday, February 13, 2007 4:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Structure reconstruction from NMR constraints? Hi, What from NMR data? Cheers, Dan.
[ccp4bb] AKTA prime
Dear all, I need to decide between buying an AKTA prime and an AKTA FPLC from GE health care. I understand AKTA prime is a low-pressure system, but because it is too much cheaper than AKTA FPLC, it is still very attractive to me. I will mainly use it for Nickel columns and gel filtration columns, and I am worried about the latter. Is it true that using AKTA prime, you can only run the 24 ml Superdex 200 column at 0.1 or 0.2 ml/min? Could anyone who has used AKTA prime give me some feedbacks? I would appreciate it. Best, Frank - Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users.
Re: [ccp4bb] Multi-copies in one assymetric unit
Sorry I forget to tell ya the details: The SG of my Data is cubic P4332. Cell is 251.34A in all three dimensions. Resolution is 3.1A. 5,6,7,8 might be the possible copies from Matthew coeficient. But I just trust 6 because Chinese like the number 6 (happy Chinese new year by the way :)). No pseudo translation judged by Native Patterson. Self-rotation at the section kappa=180 shows strong peaks at phi=45 and psi=45.At the stage of map generation, the Rfree is 42% R is 38%. Thanks! Yanming On Tue, 13 Feb 2007, Eleanor Dodson wrote: Sometimes this sort of disorder is due to an error , so the first thing is to check very carefully that the solution makes sense. Why are you so sure there are 6 copies in the asymmetric unit? In situations like this I first worry about SG. Is there a pseudo-translation vector? This can make it hard to decide on the SG.. Is there an alternate spacegroup with fewer molecules in the asymm unit? What does the self rotation show? Yanming Zhang wrote: Dear All, Maybe this is a trivial question: My data should have 6 molecules in one assymetric unit. MR could find out 4 molecules. After this, no matter how hard I have tried, no more molecules can be found. At this stage, I suppose that all other copies are dis-ordered. And go ahead to do refinement with 4 molecules (ABCD) available. The density for A is quite good. But for BCD are very dis-ordered. Many breaks in chains. I'd like to ask you: In a situation like this, should I: A, Use NCS for all copies? B Do not use NCS at all? C, Use NCS just for BCD? (even dis-ordered, but similar)? What is the trick to lower down Rfree as soon as possible, if you have experienced the same situation before? Thanks Yanming
Re: [ccp4bb] Multi-copies in one assymetric unit
Hi, Do you have any biochemical evidence that points to oligomeric nature of your protein? Does SEC indicate monomer/dimer/trimer/tetramer? If not or even if so, what does the crystal packing with your MR solution with 4 molecules suggest about monomer interactions? Does that correlate with SEC results? Assuming your SG is correct, were you doing your MR search with a monomer? Does the packing with 4 molecules leave lots of space that can be potentially occupied by more monomers? /If so, and there is indication of dimer or trimer interactions, you could try your MR again and let's say search for 3 dimers or 2 trimers or 2 tetramers/. Also, what program are you using for MR and what is the resolution range for the Rot/Trans search? If you are not using PHASER, you could /try some different variations of resolution range for the search and see if you pick up more molecules/. What kind of refinement did you do after finding the 4 molecules? Have you tried simulated annealing refinement and then inspected the resulting maps at low sigma level to see evidence for additional molecules? Also, how much sequence identity do you have between your target and search model? That can affect your map quality and R-factors quite a bit. Regards, Debanu. Yanming Zhang wrote: Sorry I forget to tell ya the details: The SG of my Data is cubic P4332. Cell is 251.34A in all three dimensions. Resolution is 3.1A. 5,6,7,8 might be the possible copies from Matthew coeficient. But I just trust 6 because Chinese like the number 6 (happy Chinese new year by the way :)). No pseudo translation judged by Native Patterson. Self-rotation at the section kappa=180 shows strong peaks at phi=45 and psi=45.At the stage of map generation, the Rfree is 42% R is 38%. Thanks! Yanming On Tue, 13 Feb 2007, Eleanor Dodson wrote: Sometimes this sort of disorder is due to an error , so the first thing is to check very carefully that the solution makes sense. Why are you so sure there are 6 copies in the asymmetric unit? In situations like this I first worry about SG. Is there a pseudo-translation vector? This can make it hard to decide on the SG.. Is there an alternate spacegroup with fewer molecules in the asymm unit? What does the self rotation show? Yanming Zhang wrote: Dear All, Maybe this is a trivial question: My data should have 6 molecules in one assymetric unit. MR could find out 4 molecules. After this, no matter how hard I have tried, no more molecules can be found. At this stage, I suppose that all other copies are dis-ordered. And go ahead to do refinement with 4 molecules (ABCD) available. The density for A is quite good. But for BCD are very dis-ordered. Many breaks in chains. I'd like to ask you: In a situation like this, should I: A, Use NCS for all copies? B Do not use NCS at all? C, Use NCS just for BCD? (even dis-ordered, but similar)? What is the trick to lower down Rfree as soon as possible, if you have experienced the same situation before? Thanks Yanming
