Dear CCP4 community: I am trying to solve a structure using Molecular Replacement. We obtained several crystal forms of the same molecule, which is a hetero-trimer(18KD+16kD+15kD). We have solved the structure of one crystal form(form_1), which has space group P 42 22, 1 molecule per Asymmetric Unit, solvent content = 60%. It has resolution 2.7A and both R values around 0.25.
Now I am trying to solve the structure of a second crystal form(form_2), which has space group P 41 22 or P 422, 2 or 3 molecules per ASU. The data has resolution around 3.3A; at 9-7A shell Chi2 around 2.5, Rlinear=0.054 and Rsquare=0.057. Completeness and redundancy are fine. However, when I tried Molecular Replacement using the solved form_1 structure as the search model, I did not get any solutions, after trying AmoRe, Molrep and Phaser. I think that probably the two (or three) molecules in one Asymmetric Unit of form_2 crystal have structural differences, and these differences are so big that MR using one single molecule just can not work (I know this sounds weird; pardon me I am a beginner). With this in mind and following other people's advice, I tried the following steps: 1) Look at the solved form_1 structure in Coot; Identify all possible combinations of two molecules that pack against each other; 2) Combine these combinations into separate new pdb files, each containing two molecules; 4) Use the new pdb files as search model for MR. I think that, if I use two molecules as a search model, probably the structural differences between the two molecules will not be so significant, because the model's size is twice increased compared to using one molecule. However, I tried all possible combinations of two molecules in AmoRe, Phaser and MolRep and still got no solutions. Cutting resolution range to 15-4A did not help either. Now I am thinking that in the Asymmetric Unit of my new form_2 crystal, maybe the two molecules' geometric relationship is not found in my solved form_1 crystal. So my question is: 1) Is there any way to find the possible geometry of two molecules in form_2 Asymmetric Unit, combine them into new pdb files and use them as MR models? 2) If I continue to use the single molecule as a MR model, should I remove some possibly flexible regions? Or just remove one or two whole monomer(s)? 3) Is it possible that the same molecule in different crystal forms have structures so different as to preclude MR trials? I appreciate any advice. Have a nice Thanksgiving. Chao
