Thank you! I would check this. However, considering that the cell can only accomodate 5-7 kDa, a polluted protein of this MW is included in our crystallization process is a considerably rare case.
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："Orr, Christian (DLSLtd,RAL,LSCI)" <0000d0fe8cd637d1-dmarc-requ...@jiscmail.ac.uk> 发送日期：2025-07-11 18:30:31 收件人：CCP4BB@JISCMAIL.AC.UK 主题：Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template Dear Chen, I would suggest a contaminant search: https://cloud.ccp4.ac.uk/manuals/html-taskref/doc.task.Simbad.html Best, Chris From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of 陈成 <0001179598b916c0-dmarc-requ...@jiscmail.ac.uk> Date: Friday, 11 July 2025 at 10:30 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template You don't often get email from 0001179598b916c0-dmarc-requ...@jiscmail.ac.uk. Learn why this is important 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 Professor School 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 This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. 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/
