[ccp4bb] AW: [ccp4bb] Improve diffraction ...any ideas?

Dear Urmi, My first question, did you collect a full data set at a synchrotron and processed this data? I think your diffraction is not as bad as you think it is, and you may get 3-3.5 Å data from it. I asume the crystal structure of the antigen is known and even with 4.5 Å data you could run

Re: [ccp4bb] Improve diffraction ...any ideas?

Use random microseeding to pick up new conditions, and work with those. See http://www.douglas.co.uk/mms.htm and http://www.douglas.co.uk/MMS_proc.htm for theory, references and practical details On 24 May 2013 03:20, Urmi Dhagat udha...@svi.edu.au wrote: Hi, I am working on a protein

Re: [ccp4bb] Improve diffraction ...any ideas?

Rajiv, I don't quite get your idea. Once the crystals of the single proteins have grown, you can't soak the other protein in, can you? Or do you mean something else? Umri, if you do get crystals of one of the components it's well worth trying cross-seeding into the complex, again using random

Re: [ccp4bb] Improve diffraction ...any ideas?

I think this is an advice not to follow. Vaheh -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajiv K Bedi Sent: Friday, May 24, 2013 1:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Improve diffraction ...any ideas? Dear Umri,

Re: [ccp4bb] Improve diffraction ...any ideas?

I think you can soak another protein into a protein crystal if it is small enough to pass through water channels, I guess. More info: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483499/

Re: [ccp4bb] Improve diffraction ...any ideas?

Hello Scott Setting up rMMS by hand works fine, but it's a bit slow and uses more protein and (sometimes much more important!) more seed stock. We recommend using a Hamilton syringe, preferably with a rounded needle, to set up by hand. 1.0 protein + 0.7 reservoir solution + 0.3 seed stock works

Re: [ccp4bb] cryo condition

Thank you everybody for their nice suggestions.. On Thu, May 23, 2013 at 7:39 PM, Matthew BOWLER mbow...@embl.fr wrote: I keep sending mails by accident today - apologies for the spam. The last sentence of my should read: This could of course be due to too high a concentration of mother

[ccp4bb] Negative FoFc around ligand

Dear users, I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang) bound to 2 ligands. After MR There is a very clear density of ligands but after refinement, I get negative fofc map near one of the ligand upto 5 sigma. However its 2fofc map covers the whole ligand. Also for the

Re: [ccp4bb] Negative FoFc around ligand

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, I assume that you carried out molecular replacement without the ligand in the search model (otherwise you are probably looking at model bias). In that case the ligand most likely has reduced occupancy. You can either manually set all

Re: [ccp4bb] Negative FoFc around ligand

Sir, I used model without ligand for MR. This happens only for some atoms not for all. So should I reduce the occupancy for all atoms? I did use occupancy refine it showed different occupancy like 0.8, 0.6 for two different atoms. Thank you Regards Kavya -BEGIN PGP SIGNED MESSAGE-

Re: [ccp4bb] Negative FoFc around ligand

Sir, I used model without ligand for MR. This happens only for some atoms not for all. So should I reduce the occupancy for all atoms? I did use occupancy refine it showed different occupancy like 0.8, 0.6 for two different atoms. I mean for the same ligand it shows occupancy of 1 for one atom

[ccp4bb] Formageddon is upon us... Important news from wwPDB!

Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about Deposition and Release of PDB Entries Containing Large Structures - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large

Re: [ccp4bb] Formageddon is upon us... Important news from wwPDB!

Perhaps a silly question: will old entries with SPLIT records be superseded by consolidated entries? And what about entries split for other reasons than size (there are only a few of those, and they are old)? Cheers, Robbie Van: Gerard DVD Kleywegt Verzonden:

Re: [ccp4bb] Negative FoFc around ligand

Kavya, Does your ligand contain any heavier atom (S, P or other)? Is it possible that your ligand binds in different orientations? So your atom X could actually be atom Y? Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree

Re: [ccp4bb] Negative FoFc around ligand

Hi Kavya, If I understand you correctly (from title and text), you meant your negative FoFc was around your ligand, is that right? I wonder if this is a case in which the ligand has an occupancy below 1, but was modeled as 1, so the refinement program had to give it a high B factor to

Re: [ccp4bb] Negative FoFc around ligand

Sir, It has two 'P's. This is the one which shows different occupancy one of them 0.64 and another 1. I checked to confirm that it is not P but water but it is too close to ligand to be water. Thank you Regards Kavya Kavya, Does your ligand contain any heavier atom (S, P or other)? Is it

Re: [ccp4bb] Negative FoFc around ligand

Sir, Yes it is around ligand. The average B-factor of one of the ligand is 36.78, of which one of the atom has occupancy B factor 0.58 39.37 0.56 38.77 0.87 37.00 Three atoms are of same type. The other ligand's overall Bfactor is 17.64. occupancy B factor

Re: [ccp4bb] Negative FoFc around ligand

Dear users, I tried giving occupancy of 0.65 and 0.6 respectively for all atoms of the two ligands and refined. Now after refinement, the atoms of ligand does not have negative density but those which did not have negative density previously appear positive. So what do I need to do? under what