Dear Devbrat,
With the unit-cell geometry you have, namely a very long axis and two
much shorter ones, you have to be exceedingly careful about how the data are
collected, and in particular about the crystal orientation and image width.
If the long axis can be brought close to being parallel to the rotation
axis - either because the crystal morphology tends to make this happen or
(better) because you can use a multi-axis goniometer to orient it that way -
the images will have rows of closely-spaced spots that should be resolvable
if the detector is placed far enough. If on the other hand the long axis is
at a large angle to the rotation axis, there will be image ranges where that
axis gets close to being parallel to the beam, so that the separation of
reflections along that long axis (in fact, along the short reciprocal axis)
will depends on their angular distance. Unless the image width is small
enough, there will be overlap of the spots for consecutive reflections along
that short reciprocal axis. Indexing diagnostics may then give an impression
that there is more than one lattice, but most of all, because two distinct
reflexions may overlap into a single spot, many integrated intensities will
be corrupted.
Perhaps this is not the case, but out of curiosity: what is the angular
width of your images?
With best wishes,
Gerard.
--
On Tue, Nov 14, 2023 at 09:25:30PM +0530, Devbrat Kumar wrote:
> Hello everyone,
>
> The issue with the crystal is its multi-lattice nature; even the truncated
> protein, which has been crystallized, exhibits multi-lattice
> characteristics (detectable only after XRD).
>
> I have multiple native and selenium datasets with similar unit cell
> parameters. (One axis is excessively long.) The XRD images were processed
> using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
> 27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data were
> integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
> CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
> suggested the presence of monomer NCS with a solvent content of 63.6%. The
> FA estimation and substructure detection were performed by SHELXC, which
> detected a very weak signal below 3.4 Å. Substructure determination was
> carried out using SHELXD, yielding a maximum figure of merit of 27.8 after
> 640 trials and suggesting 11 atoms in the substructure with an occupancy of
> at least 25%. Phasing and substructure refinement were conducted using the
> BP3 program, resulting in an FOM of 0.2. During hand determination, the
> programs suggested combined DM (density modification) FOM and phasing CLD
> score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
> choose the hand because the value is less than the threshold. Density
> modification with Fourier recycling suggests that the final FOM for hand
> one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the
> R factor and Rfree factor as 0.4262 and 0.4912.
>
> One of the MR templates (model with balbes) works(For MR, Identity with the
> PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
> Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The R
> & Rfree is not decreasing for the dataset. I have played with detector
> distances for spot resolution, but at one pHi the spots have merged as a
> single spot, while at 90 degrees will give us the streak of spots.
>
> Looking forward to hearing from you regarding dataset processing ideas for
> multi-lattice crystals(Native & Se dataset) and structure solution strategy.
>
> Thank you.
> Regards
> Devbrat
>
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