[ccp4bb] AW: [ccp4bb] Negative electron density in the Fo-Fc map at the binding site

2014-07-22 Thread Herman . Schreuder
Dear Armando, Is 1.9Å really the diffraction limit of your crystals, or do they diffract further and is 1.9Å just a convenient resolution cutoff? In the latter case you might be looking at truncation effects. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4B

[ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Bernhard Rupp
I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _c

Re: [ccp4bb] AW: [ccp4bb] Negative electron density in the Fo-Fc map at the binding site

2014-07-22 Thread Eleanor Dodson
Well yes, The bulk solvent model can distort the density, especially if the ligand is large. But it usually isnt too serious - try doing "SIMPLE" scaling and see if that has any effect on the appearance of the density Eleanor On 22 July 2014 10:16, wrote: > Dear Armando, > Is 1.9Å really the

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather tha

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Frances C. Bernstein
I took a look at both the PDB and CIF headers for the coordinates for 4C69 and they have normal looking numbers with three digits following the decimal point. According to the coordinate file header this entry was processed by PDBE. It would be interesting to hear from the PDBE staff if the stru

[ccp4bb] Off topic: Enzyme mechanism

2014-07-22 Thread Komal Pawar
Hi all, Does anybody know of a case where the same enzyme from different species, with reasonably invariant active site residues, perform identical biochemical function but have significantly different substrate binding modes/mechanism of action on the same substrate? Thanks Komal

[ccp4bb] off-topic: protein ligation and phospho-tyrosine affinity chromatography

2014-07-22 Thread Srinivasan Rengachari
Dear all,     We are planning to ligate a phospho-tyrosine containing 16aa/33aa peptide onto a 70 kDa protein and subsequently use it for crystallography studies. We will be using the Intein-fusion protein system (IMPACT kit from NEB) to accomplish the ligation. The idea is to separate the

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Zbyszek Otwinowski
Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Tim Gruene
Dear Zbyszek, when you optimise a set of parameters against a set of data, I guess you can also provide their errors. If I understand correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure

[ccp4bb] Part-time Work for Graduate Students

2014-07-22 Thread Sean Seaver
Position: P212121 is hiring graduate students for very part time work (2-3hrs/month) to help distribute product information. Job Requirements: -Know buildings on your campus other than where your lab is located -Be based in the USA About Us: We distribute scientific lab supplies and chemicals. W

[ccp4bb] Off-Topic Q / X Ray FLuoresence Scan Vs XANES

2014-07-22 Thread Tarek DawoD
Doing Fluroscence scan for protein crystal at Cu wavelength prior MAD or SAD experiment shows usually fig like this https://www.dropbox.com/s/800463dlcmws6d4/fig.png 1- Fig A should represent X ray fluorescence scan. is it the same as X ray absorption scan. what does count represent in fig A (i

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Zbyszek Otwinowski
The least-square procedure for unit cell parameter refinement provides very precise estimates of uncertainty. Why they are so precise? Because we use many thousands of unmerged reflections to determine the precision 1 to 6 parameters (unit cell parameters). However, although error propagation th

Re: [ccp4bb] Protein Crystallography challenges Standard Model precision

2014-07-22 Thread Frances C. Bernstein
Shouldn't the cell dimensions be identical in the coordinate file and in the structure factor file? In this case they are not. Frances = Bernstein + Sons * * Information Systems Consultants