2QVO.xds: Difference between revisions

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This is an example of S-SAD structure solution (PDB id [http://www.rcsb.org/pdb/explore.do?structureId=2QVO AF1382]), a 95-residue protein used by James Tucker Swindell II to establish optimized procedures for data reduction. The data available to solve the structure are two runs of 360° collected at 1.9Å wavelength.
This is an example of S-SAD structure solution (PDB id [http://www.rcsb.org/pdb/explore.do?structureId=2QVO 2QVO]), a 95-residue protein used by James Tucker Swindell II to establish optimized procedures for data reduction. The data available to solve the structure are two runs of 360° collected at a wavelength of 1.9Å.


==XDS data reduction==
==XDS data reduction==


In the course of writing this up, it turned out that it was not necessary to scale the two datasets together, using [[XSCALE]], because the structure can be solved from any of the two, separately.
In the course of writing this up, it turned out that it was not necessary to scale the two datasets together, using [[XSCALE]], because the structure can be solved from any of the two, separately. But, of course, structure solution would be easier when merging the data (try for yourself!).


===dataset 1===
===dataset 1===


Using "[[generate_XDS.INP]] ../../APS/22-ID/2qvo/ACA10_AF1382_1.0???" we obtain:
Using [[generate_XDS.INP]] "../../APS/22-ID/2qvo/ACA10_AF1382_1.0???" we obtain:
<pre>
<pre>
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
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  NUMBER OF UNIQUE ACCEPTED REFLECTIONS                13784
  NUMBER OF UNIQUE ACCEPTED REFLECTIONS                13784


So the anomalous signal goes to about 3.3 A (which is where 30% would be, in the "Anomal Corr" column), and the useful resolution goes to 2.16 A, I'd say (pls note that this table treats Friedels separately; merging them increases I/sigma by another factor of 1.41).
So the anomalous signal goes to about 3.3 Å (which is where 30% would be, in the "Anomal Corr" column), and the useful resolution goes to 2.16 Å, I'd say (pls note that this table treats Friedels separately; merging them increases I/sigma by another factor of 1.41).


For the sake of comparability, from now on we use the same axes (53.03 53.03 40.97) as the deposited PDB id 2QVO.
For the sake of comparability, from now on we use the same axes (53.03 53.03 40.97) as the deposited PDB id 2QVO.
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==SHELXC/D/E structure solution==
==SHELXC/D/E structure solution==


This is done in a subdirectory of the XDS data reduction directory (of dataset "1" or "2"). Here, we use a script to generate XDSCONV.INP (I used MERGE=TRUE, sometimes the results are better that way), run [[XDSCONV|xdsconv]] and [[ccp4com:SHELX_C/D/E|SHELXC]].  
This is done in a subdirectory of the XDS data reduction directory (of dataset "1" or "2"). Here, we use a script to generate XDSCONV.INP (I used MERGE=TRUE, sometimes the results are better that way; update Sep 2011: the [[ccp4com:SHELX_C/D/E#Obtaining_the_SHELX_programs|beta-test version of SHELXC]] fixes this problem, so MERGE=FALSE would be preferable since it gives more statistics output), run [[XDSCONV|xdsconv]] and [[ccp4com:SHELX_C/D/E|SHELXC]].  
<pre>
<pre>
#!/bin/csh -f
#!/bin/csh -f
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  shelxd j_fa
  shelxd j_fa


This gives best CC All/Weak of 37.28 / 21.38 for dataset 1, and best CC All/Weak of 37.89 / 23.80 for dataset 2, and .  
The "FIND 3" needs a comment: the sequence has 4 Met and 1 Cys, but we don't expect to find the N-terminal Met. Since SHELXD always searches for more atoms than specified, we might as well tell it to try and locate 3 sulfurs.
 
This gives best CC All/Weak of 37.28 / 21.38 for dataset 1, and best CC All/Weak of 37.89 / 23.80 for dataset 2.  


Next we run G. Sheldrick's beta-Version of [[ccp4com:SHELX_C/D/E|SHELXE]] Version 2011/1:
Next we run G. Sheldrick's beta-Version of [[ccp4com:SHELX_C/D/E|SHELXE]] Version 2011/1:
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==Availability==
==Availability==
* [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/xds-2qvo-1-1_360-F.mtz] - amplitudes  for frames 1-360 of dataset 1.
* [https://{{SERVERNAME}}/pub/xds-datared/2qvo/xds-2qvo-1-1_360-F.mtz] - amplitudes  for frames 1-360 of dataset 1.
* [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/xds-2qvo-1-1_360-I.mtz] - intensities for frames 1-360 of dataset 1.
* [https://{{SERVERNAME}}/pub/xds-datared/2qvo/xds-2qvo-1-1_360-I.mtz] - intensities for frames 1-360 of dataset 1.
* [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/xds-2qvo-2-1_180-F.mtz] - amplitudes  for frames 1-180 of dataset 2.
* [https://{{SERVERNAME}}/pub/xds-datared/2qvo/xds-2qvo-2-1_180-F.mtz] - amplitudes  for frames 1-180 of dataset 2.
* [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/xds-2qvo-2-1_180-I.mtz] - intensities for frames 1-180 of dataset 2.
* [https://{{SERVERNAME}}/pub/xds-datared/2qvo/xds-2qvo-2-1_180-I.mtz] - intensities for frames 1-180 of dataset 2.
* [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/xds-2qvo-2-1_360-F.mtz] - amplitudes  for frames 1-360 of dataset 2.
* [https://{{SERVERNAME}}/pub/xds-datared/2qvo/xds-2qvo-2-1_360-F.mtz] - amplitudes  for frames 1-360 of dataset 2.
* [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/xds-2qvo-2-1_360-I.mtz] - intensities for frames 1-360 of dataset 2.
* [https://{{SERVERNAME}}/pub/xds-datared/2qvo/xds-2qvo-2-1_360-I.mtz] - intensities for frames 1-360 of dataset 2.
 
As you can see, all these files are in the same directory [https://{{SERVERNAME}}/pub/xds-datared/2qvo/]. I put there the XDS_ASCII.HKL files and SHELXD/SHELXE result files as well.