[ccp4bb] I222 - P22121 space-group ambiguity

Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data s

Re: [ccp4bb] project and literature organization software (laboratory information management software)

2 > 8093 Zurich, Switzerland > phone: +41 44 632 68 65 > fax:+41 44 632 14 86 > web: http://www.protein.ethz.ch/people/tobias > ___ > --- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 127 Boston, MA 02115, USA Tel: 001 617 432 5601

[ccp4bb] Off-topic: Correlation of crystallographic B factors with NMR relaxation parameters

Hi everybody, Has anybody looked at possible correlation of B factors, derived from crystal structures of proteins, with relaxation parameters measured by NMR on the same type of crystals (solid-state NMR of crystals). The NMR parameters concerned are Rh1 and Rho1, which are a measure of mobili

[ccp4bb] Off-topic: 96-well plate PCR/plasmid purification

Dear All, I am looking for a bit of advice, and am interested to hear about experiences people have had with various commercially-available 96- well plate-based PCR, plasmid, and protein purification appliances and plates. Forgive me for comparing commercial vendors. We have a 96-well plat

Re: [ccp4bb] The effect of His-tag location on crystallization

Human leukotriene C4 synthase (PDB accession code: 2UUI) is another example, illustrating how an N-terminal polyhistidine-tag, in conjunction with metals, presumably facilitated crystallization. On Jun 27, 2012, at 12:04 PM, Brad Bennett wrote: I think it was an N-terminal RGS-type His tag i

Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files

- CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for

[ccp4bb] Off-topic: PDB deposition of multiple structure factor files

Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB con

Re: [ccp4bb] Substitution to glycerol during crystallogenesis

Dear Toby, I don't think there is a basic problem using glycerol in crystallization. Glycerol will affect the vapour pressure (if it is not present in the well/precipitant solution) and 10 % glycerol is ~ 1.3 molar concentration. During equilibration the drops may increase in volume, decr

[ccp4bb] xds - problem with reference profile

Dear All, I am getting a warning message in XDS I have not seen before, when trying to integrate a low resolution (~ 7 A) dataset. !!! WARNING !!! REFERENCE PROFILE # 1 IS EMPTY. THE AVERAGE PROFILE IN THIS BATCH IS USED INSTEAD. and so forth for the other reference profile

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

On Jan 30, 2012, at 10:28 AM, Jacob Keller wrote: >> I'm intrigued: how come this apparently excellent idea has not become >> standard best practice in the 14 years since it was published? > > It would seem because too few people know about it, and it is not > implemented in any software in the

Re: [ccp4bb] detect dsDNA

There exists a less toxic chemical than EtBr to stain DNA: SYBR safe DNA stain (a fluorescence dye sold by a certain vendor). Another benefit is to be able to use blue light, reducing UV/VIS light exposure when handling gels. Florian On Oct 2, 2011, at 11:49 AM, Edward A. Berry wrote: Ja

[ccp4bb] Off topic: vector map editing and DNA sequence alignment software

? What are the alternatives to above programs? Thank you in advance. Florian --- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 123 Boston, MA 02115, US Tel

Re: [ccp4bb] Electostatic surface at various pH

Hi John, I would probably use Pdb2pqr, to assign charges and radii for the atoms at different pHs, and then APBS integrated in Pymol software for visualization: http://kryptonite.nbcr.net/pdb2pqr/ http://www.poissonboltzmann.org/apbs/ Hope this helps, Florian On Aug 19, 2011, at 2:35 PM,

Re: [ccp4bb] XDS problem: REMOVE.HKL ignored?

Hi Engin, I encountered the same issue a couple of months ago. As I understand, the REMOVE.HKL file will only be used if you specify the spacegroup and unit cell in the XDS.INP file. Cheers, Florian On Jul 25, 2011, at 1:14 PM, Engin Özkan wrote: Hi all, After about a year of not worki

[ccp4bb] merge datasets

Dear All, I have two questions: 1) I have collected multiple, native datasets (5) from the same crystal (different parts of the crystals exposed with different transmission and oscillation angles). Each dataset on its own is close to complete (96-98 %). Naturally, differences in exposure,

[ccp4bb] Effect of NCS on estimate of data:parameter ratio

half the number of parameters to refine (assuming an NCS constraint)? Regards, Florian ------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US T

[ccp4bb] Problem with NCS detection in Parrot

to detect the NCS readily. Unfortunately, I don't think it is possible to input externally determined NCS operators into Parrot. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Me

[ccp4bb] Format conversion of Shelx coordinate file

, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

[ccp4bb] helix ordering upon metal binding

Dear All, Are there prominent examples of ordering of an alpha-helix within a protein upon metal binding (in particular Fe)? In my case, I observe that a 10 amino acid fragment seems to become visible in electron density maps, only upon Fe2+ binding to a glutamate (the first amino acid of

[ccp4bb] XDS - resolution limit

Dear All, Is there a way to get XDS to include reflections in the far corners of diffraction images. XDS seems to take the high-resolution limit automatically from the edge of the images corresponding to the smallest radius from the center. In my case, with the keyword set to "INCLUDE_R

[ccp4bb] Reindex and Rfree column

Dear All, I am wondering whether the Free_R column of an mtz file is altered by using "Reindex" (and/or "Cad"). The way I understand it, reindexing does not affect the Free_R column, correct? I have solved a structure with a reindexed dataset (P21212 from P22121). Now I have datasets of

[ccp4bb] Reindex and Rfree column

Dear All, I am wondering whether the Free_R column of an mtz file is altered by using "Reindex" (and/or "Cad"). The way I understand it, reindexing does not affect the Free_R column, correct? I have solved a structure with a reindexed dataset (P21212 from P22121). Now I have datasets of

[ccp4bb] arp/warp in p22121

Dear All, I am trying to build a molecular replacement model in arp/warp in space group P22121. Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far as I can see at the first Refmac refinement stage. In the log-file it says "this space group is not supp