Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, DLS, 14-16th March 2012

Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples will be held at the Diamond Light Source, UK from 13:00 March 14th to 13:00 March 16th 2012.

This series of workshops was originally concerned with the effects of radiation damage during investigation of protein structures by X-ray crystallography. Other techniques of structural biology are now being included to ensure greater information exchange. The workshop will therefore be of interest to all those using ionising radiation to examine biological structures at the molecular level.
It will consist of around 30 talks of 20-25 minutes each covering:

1.       Basic understanding of radiation damage mechanisms.

2.       Temperature-dependent (including RT) radiation damage.

3.       Reducing and mitigating radiation damage

4.       Practical aspects of managing radiation damage.

5.       Damage at new sources - XFEL

6.       Radiation damage in complementary fields

Registration and Poster Abstract submission will be open in a few weeks' time.
The cost of registration will be £100 (£120 after March 1st).
Abstract submission will close on the 1st March.

Some Abstracts will be selected for oral presentation - please indicate if you would like to be considered for this in the comments box on the registration form.

If you have suggestions for speakers, please contact Martin Weik (weik@ibs.fr) or Elspeth Garman (Elspeth.garman@bioch.ox.ac.uk).

The organizers are Robin Owen, Armin Wagner, Elspeth Garman, Martin Weik, John McGeehan, Sean McSweeney, Colin Nave, Raimond Ravelli, Gerd Rosenbaum, and Soichi Wakatsuki.

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Heads-up: PDBe service interruption 21-24 October

Dear PDBe users and depositors,

Due to essential maintenance of the computers in the campus data centre this coming weekend, all web, ftp and e-mail services of the Protein Data Bank in Europe (PDBe; pdbe.org), as well as most other EBI services, will be unavailable from Friday 21 October 11 am BST until Monday 24 October 11 am BST (*). This includes our deposition services for PDB (Autodep) and EMDB (Emdep). However, the other wwPDB and EMDB deposition sites will not be affected, so if you are in a hurry to deposit, please use the deposition services of one of our partners.

We apologise for any inconvenience this may cause.

(*) BST = British Summer Time. To convert to your local time zone, try http://www.timeanddate.com/worldclock/converter.html

--Gerard

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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK

REMINDER : CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC 30th Nov. to 4th Dec.: deadline 21st Oct

CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC

Proposal Deadline 21st October 2011

There will be beam time available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS absorbance or fluorescence spectral changes of the crystal during the X-ray diffraction experiment. Users who are interested in using this beam time (including those who are members of BAG Groups) should use the following mechanism:

_http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal _

and it must be clearly indicated in the title of the proposal form that the online monitoring of spectral changes is necessary for the project.


A brief description of the device is given below however users are encouraged to consult the web pages for detailed information:

_http://www.esrf.fr/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/Run_Your_Experiment/Microspectrophotometer_User_Guide_

The device is also described in: McGeehan, J., Ravelli, R.B., Murray, J.W., Owen, R.L., Cipriani, F., McSweeney, S., Weik, M. and Garman, E.F. (2009) Colouring cryo-cooled crystals: online microspectrophotometry. J Synchrotron Radiat., 16, 163-172.

As this is not a standard set-up, it might take a significant amount of time to train users, align the device, and analyze the data in order to derive relevant data collection schemes. We will therefore schedule 24 hours for each project. The deadline for this specific application is Friday 21st October 2011.

It is strongly recommended to, beforehand, record an absorption (fluorescence) spectrum of the crystal on a home microspectrophotometer such as the 4dx one, or at an off-line facility such as the ESRF Cryobench, and to provide it in the application form. Such a spectrum would greatly help to determine the feasibility of the experiment. For optimal experimental conditions, crystals should be frozen in minimal amounts of cryosolution, especially when the crystals are small. Finally, please note that the ESRF sample changer cannot be operated at the same time as the on-line microspec.
The use of specific LASER is possible if the device is compliant with the beam line safety system (interlock on device power).

++++++++++++
Dates of beam-time: 30th November - 4th December 2011
Storage Ring: 7/8 + 1 (200mA)
Beamline: ID14-1
Energy: 13.27 keV (not tunable)


Specifications:
UV/VIS-range: 250-1100 nm
Light source: Mikropack DH-2000-BAL (Deuterium/Halogen)
Fluorescence/Actinic excitation wavelength: 405, 440, 473, 532, 561, 671 nm
ODmax for UV-vis absorbance spectra: 2-2.5
Monitoring light size: 0.03 (min) - 0.15mm(max)
Sampling freq (to disk): 10Hz or lower

--  

help me after several refmac

From: 王瑞 <wangrui704
Date: 2011/10/13

hello everyone:

    Excuse me, could anyone give me some suggestions? Afetr several cycles of refmac, it give me such a result:               

                                       Initial    Final

                    R factor    0.2540   0.2531

                       R free    0.3499   0.3500

     Rms BondLength    0.0151   0.0151

      Rms BondAngle    2.0266   2.0393

     Rms ChirVolume    0.1179   0.1188

 In fact, I have tried model building & continue refmac, but the R free is still above 0.34. The resolution is  43.728 to  2.088Å and space group is C 2 2 21 . What I should to do? 

Thanks

----------
From: Roger Rowlett
Possibility of twinning? A simple way to check this at this point is to turn on the twin option in refmac and examine the log file. Twinning can cause you to get stuck at high R values in unaccounted for.
Roger Rowlett

----------
From: Tim Gruene

Dear ,

- - how complete is your model compared to the sequence expected in the
crystal? If it is not very complete, yet, your R-values might diverge

- - Your RMS BondAngle is pretty high. Set the matrix weight manually to a
lower number (0.1 or less) until the BondAngle is around 1.6

- - try arp/warp or any other autobuilding tool. If your data are fine,
they should produce a decent model.

Having said that you might also go back and check your data processing:
did you cut the resolution appropriately? Otherwise you may include a
lot a noise during refinement which will destabilise the refinement.

Tim

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen





----------
From: Eleanor Dodson

 In fact, I have tried model building&  continue refmac, but the R free is

Hard to say without seeing your map, model is probably correct.. Have you built waters? Are there errors? How good is your data?

 Eleanor

----------
From: Yuri Pompeu
Echoing whats been said:
1- Are you sure your crystal really is in C 2 2 21? If so How good is your data (completeness, Rmerge, etc...)
2-Could have twinning? I recently just got done working on a structure that could be scaled in C 2 2 21 but turned out to really be an almost perfect P21 twin.
(of course in monoclinic there are certain conditions for twinning...)
3- How good is your model, is it complete, all the waters? Missing protein or DNA?
 HTH

Yuri

----------
From: Pete Meyer
Similar to Tim's suggestion, but your low resolution limit may be too low (check refmac's chart of R vs resolution to confirm this).

Pete

----------
From: Xiaopeng Hu
Dear Yuri,
Could you give out the details? Such as how you found the twins?

Xiaopeng

----------
From: 王瑞 <wangrui704

After L-test,the result are follows:

TWINNING ANALYSIS:

First principles calculation of potential twinning operators using code by Andrey Lebedev:

First principles calculation has found 0 potential twinning operators

No twinning detected

<!--SUMMARY_END--></FONT></B>

$TABLE: L test for twinning:

$GRAPHS: cumulative distribution function for |L|:0|1x0|1:1,2,3,4:

$$ |L| Observed Expected_untwinned Expected_twinned $$

$$

0.000000 0.000000 0.000000 0.000000

0.050000 0.054127 0.050000 0.074938

0.100000 0.101795 0.100000 0.149500

0.150000 0.148706 0.150000 0.223312

0.200000 0.196638 0.200000 0.296000

0.250000 0.244675 0.250000 0.367188

0.300000 0.293074 0.300000 0.436500

0.350000 0.342463 0.350000 0.503563

0.400000 0.390543 0.400000 0.568000

0.450000 0.440510 0.450000 0.629437

0.500000 0.489954 0.500000 0.687500

0.550000 0.541145 0.550000 0.741812

0.600000 0.592157 0.600000 0.792000

0.650000 0.643445 0.650000 0.837688

0.700000 0.695155 0.700000 0.878500

0.750000 0.747505 0.750000 0.914062

0.800000 0.802393 0.800000 0.944000

0.850000 0.856546 0.850000 0.967938

0.900000 0.909764 0.900000 0.985500

0.950000 0.961975 0.950000 0.996313

1.000000 1.000000 1.000000 1.000000

$$

在 2011年10月13日 下午11:42，Xiaopeng Hu

----------
From: Eleanor Dodson
This Ltest certainly doesnt look twinned.

But your R factors are indictive of "mostly correct but still problems".

Didnt someone suggest running Arp-Warp to rebuild the structure?
This might reinterpret any dodgy bits.

Eleanor

Postdoctoral position, bacterial membrane protein

Postdoctoral Position Available

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Associate Professor of Biological Chemistry

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Biophysics, 3040 Chemistry Building

930 N University Ave

Ann Arbor MI  48109-1055 U.S.A.