Dear Prof Gerard Thank you for your in-depth analysis of the possibilities I am facing. The image slicing was at 0.1 degrees.
*Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 5:21 PM Gerard Bricogne <g...@globalphasing.com> wrote: > 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 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
