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
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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
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
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
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
- 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
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,
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
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 usual
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:
? 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
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
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
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,
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
Tel: 001 617 432 5602
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 Medical
,
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
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
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
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
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