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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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* 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) == | == better phases from DAD (Double Anomalous Dispersion) == | ||