[ccp4bb] Cys modification - deciding between CSS and SMC

I am working on a model at a resolution of 2.1 A. The active site Cys in both copies have a positive density towards the S end of the residue and these blobs are there in FEM and Polder maps. When I replace these residues with either CSS or SMC, I get the following statistics. What is the best w

[ccp4bb] Ligand building in real space

Dear all Is it possible to directly build a ligand in real space (in Coot?) and then generate a SMILES string for restraint generation. I have some unknown blobs in my density where they look like PEG molecules but these do not really fit the density (local CC of 0.7). I am already using Polde

[ccp4bb] Accidental crystallization of E. coli protein

During the crystallization of a totally unrelated protein from a different bacterium in E. coli, we managed to somehow crystallize an E. coli protein. It turned out to be only the catalytic domain of an enzyme. Two previous reports both used recombinant expression of this enzyme followed by limi

[ccp4bb] tNCS and PISA

I am turning again to the wisdom of the community. In a paper, the authors used a dataset in P 1 2(1) 1 displaying tNCS (not mentioned anywhere in the paper) to model a dimeric structure. At the refinement stage, they used a twin law. Looking at the PDB-REDO entry, there is a warning line - "Us

[ccp4bb] Estimate NCS copies

Dear all Is it possible to estimate the number of NCS copies by looking at reflections in the reciprocal space? If so, where can I find the details? Thanks. Mohamed

Re: [ccp4bb] How to convince oneself (and others) of ligand presence

and CC > 0.8. Can I call these 'adventitious' molecules? Thanks. Mohamed On Thu, 23 Feb 2017 13:56:05 +0000, Mohamed Noor wrote: >Dear all > >I think I have a ligand (substrate) placed in the active site of my model >correctly. The CC is 0.785, B factor of 60 A^2 which

[ccp4bb] How to convince oneself (and others) of ligand presence

Dear all I think I have a ligand (substrate) placed in the active site of my model correctly. The CC is 0.785, B factor of 60 A^2 which is roughly similar to the neighboring residues and there was no ligand in my search model*. The data extends to 2.2 A, although I think I can get something hig

[ccp4bb] Pocket identification and substrate tunnelling

Dear all I think this was discussed before on this board but I can't find the relevant thread(s), so apologies. I have a crystal structure on an enzyme with the NAD+ cofactor bound but no substrate, despite trying both co-crystallization and soaking methods and collecting datasets from 20-30 c

[ccp4bb] Salt bridge-hydrogen bonds

Dear all Is it possible for two residues to form a salt bridge between them, and at the same time**, each of them form a hydrogen bond with another residue? In other words: Arg1 - Glu10 (salt bridge) Arg1 - Tyr600 (H bond) Glu10 - Thr590 (H bond) ** I understand proteins are not static stru

[ccp4bb] autoSHARP: Am I on the right track?

Dear all Following on the previous thread on Fe-SAD, there is a solution(?) from autoSHARP with an OK-ish map and model. A quick refinement with phenix.refine gave me an R/Rfree of 28/31 % (2 A, although for the phasing run I told autoSHARP to use only up to 2.5 A). However, the model was fille

[ccp4bb] Metrics for hkl2map (Fe SAD)

Dear all I am trying to solve a structure using Fe SAD collected with mini-kappa from several non-isomorphic crystals (following on from the previous thread https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1608&L=CCP4BB&D=0&P=35088). Xtriage suggests weak anomalous signal to 4 A. For the SHEL

[ccp4bb] Off-topic: Request for DNA

Dear all I am looking for a small amount of Aquifex aeolicus DNA or cell pellet for PCR. Unfortunately neither ATCC nor DSMZ holds this bacterium. Thanks.

[ccp4bb] Point group

Dear all I can process my 3.8 A dataset in either P4 or P422 point groups. MR searches and refinement in SG P41 and P41212 results in R/Rfree of around 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to complain but Xtriage suggests 25 % twinning in the former (refinement

[ccp4bb] PISA values

Dear all I have a dimer that is related to each other by a crystallographic symmetry. My questions are: a. how reliable are the delta G values given by PISA? Has there been an experimental study? b. For a dissociation delta G of say, around 30 kcal/mol, is it possible to estimate the sort of

[ccp4bb] Refinement with phase/FOM and HL coefficients

Dear all In a few places (Refmac and Phenix, maybe there are also others), there is an option to use either phase/FOM or HL for refinement and DM. Is there any difference between these two? The dataset in question is a Fe SAD dataset. Thanks. Mohamed

[ccp4bb] PDB deposition - sequence file

Dear all The protein that was crystallized is only the first 105 residues of a 230-residue protein. In the structure, I can see density for residues 6-72. For deposition, should the whole native/biological sequence be deposited? Thanks. Mohamed

[ccp4bb] How far does rad dam travel?

Dear all In a metal-containing crystal of (say) 200 um x 200 um, and a beam size of 10 um x 10 um, how far will I need to move away from an irradiated part to a fresh part to obtain an undamaged dataset? Exposure conditions: 100 % transmission at 10^12 ph/s, 0.1 s exposure, fine sliced at 0.1

[ccp4bb] Intensities and amplitudes

Dear crystallographers Is there any reason for using one data type over the other? Are there any errors associated with the French and Wilson I-to-F conversion step? Thanks. Mohamed

[ccp4bb] Lysozyme crystals

Dear all Would anyone have nice images of lysozyme crystals in different space groups (monoclinic, triclinic and tetragonal)? Google wasn't particularly helpful... Thanks. Mohamed