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3CSL: Difference between revisions
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HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein ( | HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (HasR, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050). | ||
The ordered part of HasR has residues 112-865 and harbours 9 Met residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. 3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector. | The ordered part of HasR has residues 112-865 and harbours 9 Met residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. 3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector. | ||
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It turns out that the spot shapes are actually so irregular that XDS stops after the IDXREF step, with a long warning message. This is because it cannot index (within default error margins) enough reflections (50% is the cutoff). When that occurs, one simply continues with the step after IDXREF: | It turns out that the spot shapes are actually so irregular that XDS stops after the IDXREF step, with a long warning message. This is because it cannot index (within default error margins) enough reflections (50% is the cutoff). When that occurs, one simply continues with the step after IDXREF: | ||
JOB= DEFPIX INTEGRATE CORRECT | |||
Other than that, the three MAD wavelengths can be processed once with default parameters, as written into [[XDS.INP]] by [[generate_XDS.INP]]. This data reduction therefore proceeds in spacegroup P1, but the correct spacegroup (22) is identified by CORRECT. | Other than that, the three MAD wavelengths can be processed once with default parameters, as written into [[XDS.INP]] by [[generate_XDS.INP]]. This data reduction therefore proceeds in spacegroup P1, but the correct spacegroup (22) is identified by CORRECT. | ||
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mv GXPAM.XDS XPARM.XDS | mv GXPAM.XDS XPARM.XDS | ||
and modify XDS.INP to read | and modify XDS.INP to read | ||
JOB= INTEGRATE CORRECT | |||
Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps. | Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps. | ||
=== Peak === | === Peak === | ||
360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ | 360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames. | ||
This is an excerpt from [[CORRECT.LP]] : | This is an excerpt from [[CORRECT.LP]] : | ||
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=== High-remote === | === High-remote === | ||
Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ | Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?). | ||
From CORRECT.LP : | From CORRECT.LP : | ||
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=== Inflection === | === Inflection === | ||
360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ | 360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.8 Gb). | ||
CORRECT.LP has: | CORRECT.LP has: | ||
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== Availability of data == | == Availability of data == | ||
There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [ | There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [https://{{SERVERNAME}}/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there. | ||
=== additional information for those who want to complete the structure === | === additional information for those who want to complete the structure === | ||
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PELLAA | PELLAA | ||
</pre> | </pre> | ||
== See also == | |||
GlobalPhasing autoproc wiki http://www.globalphasing.com/autoproc/wiki/index.cgi?ACA2011Tutorial3csl | |||
GlobalPhasing autoSHARP wiki http://www.globalphasing.com/sharp/wiki/index.cgi?ACA2011Tutorial3csl | |||