Hello Professor Kay Thank you for your in-depth and valuable suggestions.
1. I used to observe multiple spots at one Phi, and at 90 degrees, I would find a streak of spots. The crystal used to be spade-shaped. The spots are visible in a count of 8 (matching the total number of crystal lattices). 2. I tried MR-SAD, but couldn't find the selenium substructure at the Sulpher position of the sequence. 3. I will follow your suggestion to read about XDS and conduct the integration using XDS. 4. If I do not find any leads, I will email you the dataset. *Warm Regards-* *Devbrat * On Wed, Nov 15, 2023 at 4:12 PM Kay Diederichs < [email protected]> wrote: > Hello Devbrat, > > your project is difficult and there is no magic bullet to solve its > problems. Your approach is good because it always pays off to process > the data carefully. > In this respect, let me make a few comments. > 1) you don't say why you call the diffraction patterns "multi-lattice". > What exactly do you mean by that? Non-merohedral > twinning? How many lattices superimposed and visible on all frames? Can > they be separately indexed by XDS > (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)? > 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling. > 3) what do you mean by "monomer NCS"? NCS implies two or more copies of > the same molecule in the asymmetric unit. > These copies often form dimers, trimers, tetramers, ... by making > more-or-less strong and specific interactions. > 4) you've advanced amazingly far and it sounds to me that with a > combination of your refined MR model with the SAD data you > should be able to improve your solution. Look up the MR-SAD pipeline (for > SAD after MR and for model rebuilding using anomalous > data) of Crank2. > > If you want me to take a look at your raw data, upload the best datasets > (native and SeMet) to a cloud service and send me the link. > > Good luck, > Kay > > On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar <[email protected]> > 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/
