SIBYLS Beamline tag:bl1231.als.lbl.gov,2007-10-26://1 2008-06-02T21:23:26Z brought to you by MAGGIE, IDAT, SBDR, and the DOE --> over 100 served Movable Type Personal 4.1 The Structures and Biochemical Activities of XPD Helicase Reveal Vital Insights into Cancer and Aging Diseases tag:bl1231.als.lbl.gov,2008://1.135 2008-06-01T21:09:41Z 2008-06-02T21:23:26Z Scott Classen http://bl1231.als.lbl.gov The structure of Sulfolobus acidocaldarius XPD has recently been solved and the biochemical activites of various disease causing mutations measured. Results are reported in the May 30th issue of Cell. LBNL has also done a nice write up.

]]> High Throughput Crystal Screening at HWI tag:bl1231.als.lbl.gov,2008://1.133 2008-05-13T15:59:54Z 2008-05-15T16:45:41Z a resource for HTS of crystallization conditions. Scott Classen http://bl1231.als.lbl.gov Burgeoning crystallographers may find the high-throughput screening (HTS) laboratory, which is part of the Center for High-Throughput Structural Biology (CHTSB) at the Hauptman-Woodward Institute (HWI) to be a very logical starting point for determining the suitability of a particular sample for macromolecular crystallography studies. The HWI will prepare crystal-growth screening experiments in 1536-well microassay plates for about $300 per sample. More details are available on their website and in the FAQ.

]]> Our detector is gone! tag:bl1231.als.lbl.gov,2008://1.132 2008-04-16T17:44:20Z 2008-05-14T21:25:02Z Scott Classen http://bl1231.als.lbl.gov It's gone! We boxed up our Q315 yesterday and sent it back to ADSC for an upgrade to the Q315r model.

 

160408_Q315gone.jpg

 

Essentially this is an upgrade to the amplifiers that read out the CCDs and the other associated electronics for getting the raw images to the detector computers for processing. The fiber optic tapers and CCDs will not be replaced. The overall benefits of this upgrade are an decrease in read-out noise, an increase in speed, and the ability to use stored dark current images. Here are some excerpts from a detailed comparison performed by James Holton:

          ampgain  eo_gain    readnoise  pixel  fog photons  allowable
detector  e-/ADU   e-/photon  e-/pixel    um      /100um2   redundancy
----------------------------------------------------------------------
Q315      12       7.3        27(swbin)  102.4     12.4         1.00
Q315       4       7.3        16(hwbin)  102.4      4.37        2.85
Q315R      4       7.3        11.5       102.4      2.26        5.51
M300HE     4?     11           7.7        73.2      1.71        7.29

"fog photons"/pixel is the number of extra background photons/pixel required to increase the noise in a pixel by the same amount as the read noise. Since the "fog photons" will add with redundancy, the far right column shows how many fold more images (relative to a Q315) you can spread the same total x-ray exposure over and get the same total read noise (as if you collected the data with "unit" redundancy on a Q315).  The Q315R will allow 5.5x more images than what we are doing now: 12 "fog photons"/pixel on a Q315 in swbin mode.

James goes on to compare the relative crysal sizes that will produce equivalent diffraction:

All things being equal (including the extent of radiation damage), the intensity of the spots and background are proportional to the crystal volume.  Doubling the crystal volume will double the signal (spot intensity) as well as double the background (in the ideal case of a "naked crystal" with no air scatter or other sources of background).  So doubling the crystal volume makes the noise (sqrt(signal+background)) go up by no more than sqrt(2).  Unless the crystal is bigger than the beam, or it is so thick that it attenuates the beam, radiation damage will be proportional to photons/um2, which has nothing to do with the crystal size.  This means that, for the same extent of damage, the signal/noise ratio goes as size^(3/2) if "size" is the linear dimension of the crystal.  That is, doubling the linear dimension of a "round" crystal will nearly triple the signal/noise (2.83x), and a 10% increase in the "size" (linear dimension) will increase signal/noise by 15%.

If we have some high-res spot with I/sig(I)=2 in the absence of any background or read noise, then there are (on average) 4 photons in that spot (4/sqrt(4) = 2).  Spots typically take up on the order of 25 pixels.  So, adding 0.1 "fog photon"/pixel (as on a Mar300HE) will make I/sig(I) of this spot drop from 2.0 to 4/sqrt(4+25*0.1) = 1.6.  Increasing the crystal size by 12.5% will increase the crystal volume by 42% and put 5.7 photons into this same spot (for the same exposure time and therefore the same amount of radiation damage) and bring I/sig(I) back up to 5.7/sqrt(5.7+25*0.1) = 2.0.  This means that the crystal size needed to achieve a given resolution limit on the Mar300HE is 12.5% larger than the crystal size needed to achieve the same resolution with an ideal photon-counting detector (such as the Pilatus). This is assuming there are no other sources of noise, including x-ray background.

Changing the read noise to 2 "fog photons"/pixel will make the I/sig(I) of this 5.7-photon spot drop from 2 to (5.7/sqrt(5.7+25*2)) = 0.76.  Bringing the signal up to 16.3 photons/spot will bring I/sig(I) up to 2.0 again.  This represents a ~3-fold increase in crystal volume (16.3/5.7=2.86) and a 42% increase in crystal size.  To put it another way, using the Mar300HE instead of a Q315R would let us get away with crystals 30% smaller in linear dimension for a given resolution limit (and given amount of damage).  Going from a Q315R to a Q315 (with 21 "fog photons"/pixel) will require 47.9 photons in the spot (47.9/sqrt(47.9+25*21) = 2.0) and another 43% increase 

detector    photons/spot   xtalsize
perfect          4.0     0.63 or -37%
M300HE           5.7     0.71 or -29%
Q270             7.8     0.78 or -22%
M300            12.2     0.91 or -9%
Q315R           16.3     1.00
Q315            47.9     1.43 or +43%

The take home message is that our new Q315r will be way better than that old Q315 peice of junk. We will now collect more accurate data in less time with smaller crystals.

 

]]> NIH now requires open-access to manuscripts tag:bl1231.als.lbl.gov,2008://1.131 2008-04-11T21:39:15Z 2008-04-11T21:44:05Z Scott Classen http://bl1231.als.lbl.gov As of Monday April 7th -

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law. [FULL TEXT]

]]> Crystals webapp Installed tag:bl1231.als.lbl.gov,2008://1.126 2008-03-26T16:53:17Z 2008-03-26T21:59:30Z The crystals server (an Apache Tomcat webapp) has been installed. The crystals webapp will allow you to upload an excel spreadsheet, containing a list of samples, to the SIBYLS beamline for use with DOMO. The spreadsheet will be automatically converted... Scott Classen http://bl1231.als.lbl.gov The crystals server (an Apache Tomcat webapp) has been installed. The crystals webapp will allow you to upload an excel spreadsheet, containing a list of samples, to the SIBYLS beamline for use with DOMO. The spreadsheet will be automatically converted to an XML file and will become available to you via Blu-Ice once you start data collection. The webapp was developed at the SSRL and is in use at their Macromolecular Crystallography facility. If you have used the SAM robot at Stanford and uploaded your spreadsheet to their server then you will notice a distinct similarity.

]]> Yeast Topoisomerase II bound to DNA tag:bl1231.als.lbl.gov,2008://1.122 2008-03-26T16:02:54Z 2008-03-26T17:13:52Z As recently reported in the ALSNews: “The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab... Scott Classen http://bl1231.als.lbl.gov As recently reported in the ALSNews:

“The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II topoisomerase (topo II) that is responsible for untangling coiled strands of the chromosome during cell division. Preventing topo II from disentangling a cell’s DNA is fatal to the cell, which is why drugs that target topo II serve as agents against bacterial infections and some forms of cancer. This first ever structural image of topo II should help in the development of future antibacterial and anticancer drugs that are even more effective and carry fewer potential side effects.”

The original publication in Nature can be found here: K.C. Dong and J.M. Berger, “Structural basis for Gate-DNA recognition and bending by type IIA topoisomerases,” Nature 250, 1201 (2007).

]]> The Wonderful World of Early Computing tag:bl1231.als.lbl.gov,2008://1.121 2008-02-27T06:44:10Z 2008-03-07T18:03:12Z Brief but interesting history of early computers On September 9, 1945, U.S. Navy officer Grace Hopper found the first computer “bug”: a moth stuck between the relays on the Harvard Mark II. She noted it on her log as the... Scott Classen http://bl1231.als.lbl.gov Brief but interesting history of early computers

On September 9, 1945, U.S. Navy officer Grace Hopper found the first computer “bug”: a moth stuck between the relays on the Harvard Mark II. She noted it on her log as the “first actual case of bug being found.” Though the term “bug” had meant a computer error beforehand, it became a popular term after this incident.

]]> The Protein Data Bank now requires your experimental data tag:bl1231.als.lbl.gov,2008://1.119 2008-01-31T16:59:50Z 2008-01-31T17:12:01Z The Protein Data Bank is requiring, effective February 1, 2008 (i.e. tomorrow), that structure factor amplitudes/intensities for crystal structures must be deposited along with model coordinates. So if you need some structure factors to go along with your PDBs we... Scott Classen http://bl1231.als.lbl.gov The Protein Data Bank is requiring, effective February 1, 2008 (i.e. tomorrow), that structure factor amplitudes/intensities for crystal structures must be deposited along with model coordinates. So if you need some structure factors to go along with your PDBs we can help you out. Apply for beamtime via the red “GENERAL USER PROPOSAL” link in the side bar to the right.

]]> New DOMO Sample Dewar Lid tag:bl1231.als.lbl.gov,2007://1.109 2007-12-21T18:52:05Z 2008-05-14T21:56:17Z We've installed a sweet new blue anodized aluminum air dam on the pneumatic lid for the DOMO sample dewar (with color coordinated electric blue CPU fans). The air dam helps to draw off frozen ice crystals from the air above... Scott Classen http://bl1231.als.lbl.gov 211207_dewar.jpg]]> Detergents that may be useful for your SAXS experiment tag:bl1231.als.lbl.gov,2007://1.106 2007-12-12T02:03:05Z 2007-12-13T19:11:30Z Quen Cheng in the Cooper lab has done a nice set of experiments to address the usefulness of various readily available detergents for improving the behavior proteins in SAXS experiments.... Scott Classen http://bl1231.als.lbl.gov Quen Cheng in the Cooper lab has done a nice set of experiments to address the usefulness of various readily available detergents for improving the behavior proteins in SAXS experiments.

]]> Publications in 2007 tag:bl1231.als.lbl.gov,2007://1.101 2007-12-09T04:51:06Z 2007-12-13T18:05:12Z At least 18 publications were made possible by the SIBYLS beamline in 2007 and have been added to our publications page. We are very pleased that the PX and SAXS endstations have been so useful to so many researchers doing... Scott Classen http://bl1231.als.lbl.gov At least 18 publications were made possible by the SIBYLS beamline in 2007 and have been added to our publications page. We are very pleased that the PX and SAXS endstations have been so useful to so many researchers doing such varied work. We hope that 2008 will be even more productive. If you know of any publications that we have not included please let us know.

]]> DOMO Does Remote Too tag:bl1231.als.lbl.gov,2007://1.96 2007-11-10T01:25:51Z 2007-11-10T01:51:05Z DOMO used to collect data remotely for the first time. Scott Classen http://bl1231.als.lbl.gov DOMO (Dynamic Offsite MX(Macromolecular Crystallography) Operator) mounted crystals remotely for the first time today. The user accessed the beamline via port 22 (i.e. ssh) from San Diego using NX Client and was able to successfully screen through 50 or so crystals. Although I could have monitored the shift from my office, from home, or from Tahiti, I thought it would be more prudent to remain close to the beamline in the unlikely event that intervention was needed…. Well I’m glad that I stuck around. Although DOMO performed well, there were a couple of times that I needed to step in a make things right. Overall, however, it was a very successful first run.

If you are interested in collecting crystallographic data from the comfort of your own lab (or Tahiti) I would encourage you to apply for time on the SIBYLS beamline. We have a small supply of sample cassettes and the necessary tools for loading the cassettes. A cassette kit can be sent to you, whereupon you load the cassette with your valuable samples, and thusly send it back to the beamline in time for your shift. It’s loads of fun!

]]> The Fastest Windows Vista Notebook tag:bl1231.als.lbl.gov,2007://1.92 2007-10-30T05:37:13Z 2008-01-11T19:41:22Z This is pretty funny... Scott Classen http://bl1231.als.lbl.gov This is pretty funny]]> Review of SAXS combined with crystallography and computation tag:bl1231.als.lbl.gov,2007://1.32 2007-10-23T18:10:02Z 2008-01-09T18:37:14Z A new review on macromolecular SAXS has been published in the Quarterly Reviews in Biophysics by Putnam, C.D., Hammel, M., Hura, G.L., and Tainer, J.A."This six part review addresses both theoretical and practical concepts, concerns and considerations for using these... Scott Classen http://bl1231.als.lbl.gov A new review on macromolecular SAXS has been published in the Quarterly Reviews in Biophysics by Putnam, C.D., Hammel, M., Hura, G.L., and Tainer, J.A.


"This six part review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures."


The review is available for download and is an extensive and up-to-date review on the application of small angle X-ray scattering.

]]> The Gel Dilemma tag:bl1231.als.lbl.gov,2007://1.31 2007-10-19T04:08:27Z 2008-01-11T19:42:15Z Rands is even more obsessed about his writing instruments than Jane and I.... Scott Classen http://bl1231.als.lbl.gov Rands is even more obsessed about his writing instruments than Jane and I.

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