Re: [ccp4bb] ATP analog

Dear Adriana, this depends on the enzyme i.e. does your enzyme hydrolyse the alpha-beta or beta-gamma bond? If it hydrolyses the beta-gamma bond, options mentioned are indeed: -AMPPNP (Adenylyl-imidodiphosphate) -AMPPCP(β,γ-Methyleneadenosine 5′-triphosphate)* *-AMPPP(S) (ATP-γ-S) -ADP-BeFx

[ccp4bb] Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing

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Re: [ccp4bb] ATP analog

Hi, one word of caution with Metal fluoride complexes. Though they can provide valuable inside in the reaction mechanism, even better than some ATP-analogues, one has to be careful what metal to use to get the right complex. See review below, which summarises the problems which can occur,

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I've just started decommissioning our aged Rigaku X-ray system prior to replacement and before I consign every bit to surplus and the scrap yard there's a possibility that someone else in the USA is nursing an old RuH3R/RaxisIV++ system and could find use for a board or TMP controller or ...

Re: [ccp4bb] peroxy-glutamate?

Thanks to all who replied. Yes, in some of the other cases density between Cd and Cg is conspicuously weak. From preliminary tests it looks like dual conformations, in some cases together with correlated waters, will account for the density adequately. No Zebras here! eab On 05/03/2017 04:26

Re: [ccp4bb] peroxy-glutamate?

Dear Ed, Have you considered the possibility that it could be a water stepping in to fill the void created by partial decarboxylation of the glutamate? That could be easily modelled, refined, and tested for its ability to flatten the difference map. Gerard. -- On Wed, May 03, 2017 at

Re: [ccp4bb] peroxy-glutamate?

Dear Ed, Thank you for the picture. The decarboxylation of GLU and ASP side-chains is perhaps the most ubiquitous manifestation of radiation damage. We have introduced a feature in our autoPROC processing package whereby, if redundancy in the unmerged data is sufficient to allow reasonably

Re: [ccp4bb] peroxy-glutamate?

On 05/03/2017 02:46 PM, Gerard Bricogne wrote: Dear Ed, Have you considered the possibility that it could be a water stepping in to fill the void created by partial decarboxylation of the glutamate? That could be easily modelled, refined, and tested for its ability to flatten the

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Re: [ccp4bb] peroxy-glutamate?

Dear Gerard, I am sure others > are certain to propose a cooler name for that very same type of map > some day ;-) . > a free tip: how about DDM (Decarboxylation Detector Map)? All the best, Pavel

Re: [ccp4bb] peroxy-glutamate?

Peroxyacids are unlikely - they're very reactive/unstable under normal conditions. Is it possible your crystal is just at unusually low pH so these acids are protonated? That makes the carbon-oxygen bond lengths asymmetric, possibly by enough to explain your blobs. Tristan Tristan Croll

[ccp4bb] HETATM record after Refmac

Dear ccp4ers, is there way to retain HETATM keyword for ligands when running refmac? It apparently changes HETATM to ATOM which spoils some nice ligand features in Coot... Best regards, Jan

Re: [ccp4bb] ATP analog

Thanks every one for the great help. I am loaded with all the useful information. best Adriana On Tue, May 2, 2017 at 9:07 PM, Deaconescu, Alexandra < alexandra_deacone...@brown.edu> wrote: > Hi, > > ATPgS is an option, but it is slowly hydrolysable, so depending on your > enzyme, it might not

Re: [ccp4bb] HETATM record after Refmac

Indeed, even from i2. The issue is somewhere else, sorry for blaming refmac. Jan On 05/03/2017 01:09 PM, Robbie Joosten wrote: Hi Jan, That could be a postprocessing thing, because that version of Refmac works fine from the command line or from CCP4i (at least in my hands on Linux). Cheers,

Re: [ccp4bb] peroxy-glutamate?

Damage-Selective (DamSel) map? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bellini, Dom Sent: Wednesday, May 03, 2017 6:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? or RDM (raddam detection map), better known as raddamap? :) BW, D