[ccp4bb] Duax High School Program | Hauptman-Woodward Medical Research Institute

Colleagues, This workshop is virtual this summer, and therefore available to students worldwide. Please share with your student science enthusiasts. -Lisa Lisa J Keefe, PhD IMCA-CAT Industrial Macromolecular Crystallography Association - Collaborative

Re: [ccp4bb] Molecular replacement problem

Hi Robert, In addition to the great suggestions you already have received, maybe you should also consider SIMBAD or similar programs? The behavior you are describing is typical of, albeit not exclusive to, having crystallized a contaminant protein. Good luck! Nukri On Thu, Jun 18, 2020, 08:01

Re: [ccp4bb] AW: Molecular replacement problem

Robert, it would be very interesting to know your cell dimensions and corresponding N. mol. per AU to see if it's trying to be another space group. How long did the crystals take to grow? You could also try Contaminer and Simbad ;-)Jon CooperOn 18 Jun 2020 14:38, "Schreuder, Herman /DE" wrote:

Re: [ccp4bb] Molecular replacement problem

It may be worth trying rigid body-refinement of the solution, using two rigid bodies, one per monomer, if you haven’t tried already. Then perform positional refinement. When refining with the original sequence, first remember that R/Rfree are bound to be and stay high with at most 25%

[ccp4bb] AW: Molecular replacement problem

Dear Robert, In addition to the remarks and suggestions by others: How do your electron density maps look like? Do they look remotely reasonable, or do they look like they had gone through a meat grinder? If they look remotely ok, you could also try manual rebuilding, pruning etc. However, if

Re: [ccp4bb] Molecular replacement problem

Or try the other orthorhombic SGs..? Some general ideas for any such problem... Is there evidence for a dimer in the asymmetric unit, or could your dimer be generated by the crystal 2-folds? Checks on data - all easily accessed from CCP4I2 .. First is the data OK - Wilson plot? twinning? r

Re: [ccp4bb] Molecular replacement problem

I managed to solve a structure by MR at 2.4 A with a 27% identity model. Like you, I had to use a dimer search model to make any headway. To get usable maps and an initial model, I used Chainsaw to truncate the search model, Phaser (MR), Parrot (DM) with NCS averaging, then auto building with

Re: [ccp4bb] Molecular replacement problem

Hi Robert, Have you tried lower symmetry spacegroups? Maybe your crystal is 'almost-but-not-quite' orthorhombic and is in fact monoclinic, pretending to be orthorhombic. Zanuda can do this for you. https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Good luck, Dave

[ccp4bb] Molecular replacement problem

I've been pulling out my hair with this for a few months now. I have data sets to 2.6 A for a new enzyme in the aminotransferase superfamily. Unfortunately, the closest structure is only 25% identity. MR with PHASER using the monomer was a complete failure. Since the minimum structure of