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1Y13: Difference between revisions
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The structure is [http://www.rcsb.org/pdb/explore/explore.do?structureId=1Y13 deposited] in the PDB, solved with SAD and refined at a resolution of 2.2 A in spacegroup P4(3)2(1)2 (#96). | The structure is [http://www.rcsb.org/pdb/explore/explore.do?structureId=1Y13 deposited] in the PDB, solved with SAD and refined at a resolution of 2.2 A in spacegroup P4(3)2(1)2 (#96). | ||
The data for this project were provided by Jürgen Bosch (SGPP) and are linked to [http://bl831.als.lbl.gov/example_data_sets/ACA2011/DPWTP-website/index.html the ACA 2011 workshop website] and [ | The data for this project were provided by Jürgen Bosch (SGPP) and are linked to [http://bl831.als.lbl.gov/example_data_sets/ACA2011/DPWTP-website/index.html the ACA 2011 workshop website] and [https://{{SERVERNAME}}/pub/xds-datared/1y13/ here]. | ||
There are two high-resolution (2 Å) datasets E1 (wavelength 0.9794Å) and E2 (@ 0.9174Å) collected (with 0.25° increments) at an ALS beamline on June 27, 2004, and a weaker dataset collected earlier at a SSRL beamline. We will only use the former two datasets here. | There are two high-resolution (2 Å) datasets E1 (wavelength 0.9794Å) and E2 (@ 0.9174Å) collected (with 0.25° increments) at an ALS beamline on June 27, 2004, and a weaker dataset collected earlier at a SSRL beamline. We will only use the former two datasets here. | ||
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thus proving that both datasets were interrupted for 20 minutes around frame 370. | thus proving that both datasets were interrupted for 20 minutes around frame 370. | ||
Interestingly, both datasets appear to be collected at the same time, but at different wavelengths (E1 at 0.9794 Å, E2 at 0.9184 Å), and yet the individual parts merge as follows: using the following | Interestingly, both datasets appear to be collected at the same time, but at different wavelengths (E1 at 0.9794 Å, E2 at 0.9184 Å), and yet the individual parts merge as follows: using the following XSCALE.INP: | ||
UNIT_CELL_CONSTANTS=103.316 103.316 131.456 90.000 90.000 90.000 | UNIT_CELL_CONSTANTS=103.316 103.316 131.456 90.000 90.000 90.000 | ||
SPACE_GROUP_NUMBER=96 | SPACE_GROUP_NUMBER=96 | ||
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R_meas mapped on the detector, showing elevated R_meas at the location of the ice rings. | R_meas mapped on the detector, showing elevated R_meas at the location of the ice rings. | ||
== Solving the structure == | == Solving the structure with pseudo-SAD == | ||
It appears reasonable to discard the "second parts" since they are strongly influenced by radiation damage. Then, we could | It appears reasonable to discard the "second parts" since they are strongly influenced by radiation damage. Then, we could | ||
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# keep the first parts of E1 (inflection, according to the documentation) and E2 (high-enery remote) separate, and treat them as MAD (or rather, DAD). | # keep the first parts of E1 (inflection, according to the documentation) and E2 (high-enery remote) separate, and treat them as MAD (or rather, DAD). | ||
=== First try | === First try === | ||
Let's look at the XSCALE statistics for the merged-together "firstparts": | Let's look at the XSCALE statistics for the merged-together "firstparts": | ||
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[[File:1y13-raddam-contrast-raddam.png]] | [[File:1y13-raddam-contrast-raddam.png]] | ||
== Automatically building the main chain of 452 out of 519 residues == | === Automatically building the main chain of 452 out of 519 residues === | ||
Based on the sites obtained by SHELXD, we run | Based on the sites obtained by SHELXD, we run | ||
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At this point the structure is obviously solved, and we could use buccaneer or Arp/wArp to add side chains and the rest of the model. 3-fold NCS surely helps! | At this point the structure is obviously solved, and we could use buccaneer or Arp/wArp to add side chains and the rest of the model. 3-fold NCS surely helps! | ||
== Could we do better? == | === Could we do better? === | ||
Yes, of course (as always). I can think of four things to try: | Yes, of course (as always). I can think of four things to try: | ||
* an [[optimization]] round of running xds for the two datasets | * an [[optimization]] round of running xds for the two datasets | ||
* using a negative offset for STARTING_DOSE in XSCALE.INP, as documented in the [[XSCALE]] wiki article. | * using a negative offset for STARTING_DOSE in XSCALE.INP, as documented in the [[XSCALE]] wiki article. | ||
* use MERGE=TRUE in XDSCONV.INP. I tried it and this gives 20 solutions with CCall+CCweak > 25 out of 1000 trials, whereas MERGE=FALSE (the default) gives only 4 solutions! | * use MERGE=TRUE in XDSCONV.INP. I tried it and this gives 20 solutions with CCall+CCweak > 25 out of 1000 trials, whereas MERGE=FALSE (the default) gives only 4 solutions! Update Sep 2011: the [[ccp4com:SHELX_C/D/E#Obtaining_the_SHELX_programs|beta-test version]] of SHELXC should have a fix for this. | ||
== better phases from DAD (Double Anomalous Dispersion) == | |||
The reason why pseudo-SAD is described here first is that, historically, I did it first since I thought that the wavelength could not realistically be changed within 3 seconds, and I therefore thought that the headers were wrong and this would not actually be a two-wavelength experiment. Along these lines, I interpreted the correlation coefficient of 1.0 between the E1 and E2 first parts as indicating that no isomorphous difference exists. | |||
The | In a discussion with Gerard Bricogne and Clemens Vonrhein after the ACA2011 workshop it turned out that my theory, which claims that E1 and E2 are actually the same wavelength, is wrong. This was investigated by looking at the difference map (obtained using phenix.fobs_minus_fobs_map) of E1 and E2 (taking the first parts in each case) phased with the 1y13 model, which shows three strong (14-19 sigma) peaks. The fact that the 1-370 pieces merge so well seems to be a consequence of the fact that the anomalous signal of the two wavelengths is so similar, and the dispersive difference between the wavelengths does not significantly decrease the high correlation coefficient in data scaling. | ||
In a discussion with Gerard Bricogne and Clemens Vonrhein after the ACA2011 workshop it turned out that my theory, which claims that E1 and E2 are actually the same wavelength, is wrong. This was investigated by looking at the difference map (obtained using phenix.fobs_minus_fobs_map) of E1 and E2 (taking the first | |||
Thus | Thus even better phasing would be obtained by keeping the wavelengths separate and doing MAD (in fact DAD) - but zero-dose extrapolation could and should be done in the same way. I've therefore continued the analysis in [[1Y13-DAD]]. | ||