The first time for me to know this information. I would check this as you suggested~~
chen Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai District, Tianjin 300072, China 天津市南开区卫津路92号,天津大学生命科学学院15教学楼, 邮编:300072 发件人："Rudolph, Markus" <[email protected]> 发送日期：2025-07-11 20:05:04 收件人："陈成" <[email protected]> 主题：Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template Hello Chen,running your two cells through a search using the reduced cells turns up nothing special, except 8bq3, a SH3-domain. When dealing with peptides and crystallization conditions are right (e.g. high P400 or MPD, extremes of pH - depending on the peptide sequence), it is possible to induce an alpha-helix that crystallizes. We had such a case and described it in PMID 25866655. At the time, we used Arcimboldo to determine the structure, but if you assume a helix, playing with different-size helices as search models may turn out useful. Also, the self-rotation function may be informative as you have space (in P622) for 5-6 kDa of mass, i.e. 44-53 residues. If there is a helix bundle sitting on an NCS axis close to one required for higher metric symmetry, the space group may need to be relaxed, and you did that already, so the datasets in different space group symmetries and space groups (all screw variants) are ready. Good luck, Markus On Fri, Jul 11, 2025 at 11:30 AM 陈成 <[email protected]> wrote: Dear CCP4BB people, I have been working on several data sets collected from crystals grown in co-crystallization trials containing a small molecule and Calprotectin, a heterologous protein dimer comprised of two polypeptides with around 90 and 120 amino acids respectively. The crystallographic structure of Calprotectin complexed with a 18-aa peptide have been deposited in RCSB database under PDB entry 7QUV, with cell parameters a = b = 50.8, c = 148.8 in the P 32 2 1 space group. On the contrast, the bunches of data sets I collected give cell parameters a = b = 38.3, c = 196.3 in the P 6 2 2 space group when an oscilliation angle of 0.5 degree was used or cell parameters a = b = 38.2, c = 149.0 in the P 6 2 2 space group when an oscilliation angle of 0.2 degree was used. In either cases, Matthews_coef analysis would suggest that the crystal cell cannot accommodate the whole Calprotectin complex. I had used each single protein of Calprotectin as the search template for MR, but failed as well. Though Phenix.xtriage suggest nothing wrong with the data sets, however, considering that the two polypeptide conprising Calprotectin is structurally similar, I had also tried indexing the data sets under space group spanning P2, P3 apart from P622 and then run MR by a thorough combination of each data sets and different template choices, which, in opposition to what was expected, still gave no reliable MR solution. It's noteworthy that the diffraction pattern of my crytals seemingly showed that multi-crystal problem or other intrinsic growth defects might be underconsidered. In fact, I've been encountering the above crystallographic situation for 3 times recently, which all bear the following characteristics: (1) cell volume is far smaller than expected for containing targeted macromolecules (protein/DNA) that is used for crystallization. (2) no MR solution is achieved though MR template is extremely and sometimes 100% similar. (3) growth defects such as multi-crystal or fibrous diffraction problems possibly exist. Hopefully someone may have dealt with such issues before. Any suggestions is welcomed! Sincerely Chen Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai District, Tianjin 300072, China To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
