Re: [ccp4bb] Occupany refinement protocol amd best practices

Hi Matt, Im wondering about occupancy refinements - both what's going on under the > hood and what are best practices. > since you are quoting Phenix I suggest this bit of reading that is somewhat relevant to your questions: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter

[ccp4bb] Occupany refinement protocol amd best practices

Hi all, Im wondering about occupancy refinements - both what's going on under the hood and what are best practices. In the example I have, there is a ligand found in two distinct, partially overlapping sites that can be modeled is some confidence, but likely there are very low occupancy additi

Re: [ccp4bb] Fragile Crystals

Hi Elizabeth, As suggested VMXi at Diamond may be able to help with in situ data collection without harvesting. I'd be happy to discuss if useful? cheers Mike Sent from Outlook for Android From: CCP4 bulletin board on behalf of CCP4BB

Re: [ccp4bb] Quaternary Structure concept

Hello, it sounds like a monomeric protein which has been cleaved in 4 places so that would not give it 'quaternary' structure. If the nicked monomers assembled into dimers or timer, etc, then it becomes quaternary. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobil

Re: [ccp4bb] Fragile Crystals

Hi Sorry if someone else has mentioned this already, but how about shooting your crystals in situ (i.e. while sitting in the plate)? I know that VMXi at Diamond can do this (in fact it's designed for his purpose) but haven't collected data in long enough not to know if it can be done elsewhere.

[ccp4bb] Quaternary Structure concept

Dear CCP4BB comunnity; I am not a structural biologist thus far. I would like to inquire about the concept of quaternary structure and its applicability to the system I am currently investigating. The protein under study is a human lysosomal protein (Gene MAN2B1) that initially presents as a sing

Re: [ccp4bb] Fragile Crystals

Hello Morgan In addition to the other good suggestions, I have a few observations of my own. If your crystals crack without handling or adding anything to the drop, then they are extremely environment-sensitive. If that's the case, testing at room temperature will be problematic because tha

Re: [ccp4bb] Fragile Crystals

Hi Morgan Elizabeth, Just following up on Vaheh’s suggestion, you can also add 2-4% of cryoprotectant, which includes your mother liquor (and your protein if crystals have dissolved), into the crystallization drop daily or weekly after crystals appear. Repeat this step until reaching the desire

Re: [ccp4bb] Fragile Crystals

Hi Morgan Elizabeth, In some cases adding 1-2% of cryoprotectant into crystallization drop during setting those drops up helps to introduce 25-30% of the same cryoprotectant during harvest, provided you still can get those crystals to grow. Worked for me in several cases. Vaheh From: CCP4 bul

Re: [ccp4bb] Fragile Crystals

Hi Blake, You can cross seed and get new condition with good stable crystal system. Also you could try VMXi beamline, you do not need to use cryo and use the plate directly.. You have to use Greiner Crystal QuickX ™ or MiTeGen In-Situ-1 ™ plates. Thanks Kannan Show quoted text On Wed, 22 Nov

Re: [ccp4bb] Fragile Crystals

Hi Morgan, Some of the things that you could try with the conditions that you have already found: 1) Lower the temperature for incubation, which might slow down crystal formation and decrease potential defects as the crystals form 2) Harvest the crystals using a humidity control device like th

Re: [ccp4bb] Fragile Crystals

There are multiple avenues you could explore. If you think handling is an issue, you could look into growing and collecting with "in situ" plates. You could test for diffraction at room temp, or even get a full data set at room temp by combining data from multiple crystals. If diffraction is n

Re: [ccp4bb] Fragile Crystals

Hi Morgan, Have you tried MMS? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157405/ If you can reproducibly grow crystals MMS might give you hits in different conditions during screening. I’ve used this successfully multiple times for crystals that wouldn’t optimize with standard methods. We we

[ccp4bb] Fragile Crystals

Hello! I am a PhD student working on a crystallography project to wrap up my dissertation research. I have purified a complex of two proteins, and I can consistently grow crystals in 10% PEG3350, 0.2M KSCN, 0.1M BIS-TRIS propane pH 7.5. These crystals have sharp edges and can grow to a large si

Re: [ccp4bb] low resolution data refinement

Dear Liu, If you are really confident in your MR solution some good tools to refine low resolution structures are LORESTR pipeline and iSOLDE software. Best. Michel. > Le 21 nov. 2023 à 13:03, Yahui Liu a écrit : > >  > Dear all, > I got a protein crystal dataset of 4.3 A and would like to

Re: [ccp4bb] low resolution data refinement

Not sure if it's been mentioned that NCS can help a lot at that resolution. We did some mutants derived from a 2 Angstrom native structure at about that resolution with 4-fold NCS and the maps were quite convincing, well, I thought anyway. That was in the days of RESTRAIN which, I think, had an

[ccp4bb] ECA lunchtime webinar

Dear all, on the 23rd November 2023 at 13:00 CET Dr. Tatjana Barthel (HZB Berlin) will present a talk on "Crystallographic Fragment Screening at the HZB - Workflow, Tools and Procedures" as part of the ECA Lunch webinar series. You can register for the webinar here: https://www.eventbrite.com/

[ccp4bb] Postdoc CNRS Bordeaux

Dear all, · A Postdoctoral position is available in the laboratory of Nico Reyes at the CNRS in Bordeaux, France. We are an international team working on novel functional and pharmacological mechanisms of human membrane proteins. We combine functional and biophysical approaches (ITC, f