3CSL: Difference between revisions

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.  

 

HasA/R crystallizes in spacegroup F222; cell parameters are a=157Å, b=163Å, c=596Å. There are 2 complexes per ASU. Data to about 3.0Å could be collected from one crystal, which was translated between wavelengths. The anomalous data are useful to about 5Å only. These MAD data correspond to a structure with an average B of 100 Ų; the project is challenging for humans, and currently too difficult for automatic methods of structure solution and model building.  

The deposited 3CSL structure was not obtained from these MAD data alone, but the model was actually refined against slightly better (2.7Å) data collected on a native crystal at the ESRF. Altogether there are 1852 residues and two heme molecules in the ASU.

  JOB= DEFPIX INTEGRATE CORRECT  

  JOB= INTEGRATE CORRECT

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.

Next, we can use [[xdsstat]] to get frame-wise statistics from XDS_ASCII.HKL:

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?).

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).

These correlations are worse than what I like to see from MAD datasets. One might think that some of the badness is maybe due to the fact that we used an unrealistic high-resolution limit, but if we use INCLUDE_RESOLUTION_RANGE=50 3.2 (this has to given three times, after each of the INPUT_FILE lines) the correlations are exactly the same.

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.