You seem pretty near to having solved your structure! Ignoring the data problems..
Extra steps I might have used. 1) Self rotation function. (in CCP4I2 the task is under data analysis ..) Does it suggest a NCS operator? If so is this a two fold? which might mean you have a dimer.. 2) Now you have a reasonable R factor try extending the resolution. the refinement program will weight down the high resolution less reliable data but the extra information might marginally improve the maps. 3) Use the calculated phases to run an anomalous map - REFMAC will produce the appropriate coefficients and you can display the map in COOT. Do a peaksearch and you should of course see the sites SHELX found.. But sometimes you get peaks over S atoms and that makes you pretty confident that the sequence there is correct. On Wed, 15 Nov 2023 at 10:42, Kay Diederichs <kay.diederi...@uni-konstanz.de> 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 <devformed...@gmail.com> > 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/
