Hi. When in doubt, reprocess in P1. That has cleared things up on more than one occasion.
Ala Ala M Shaqra, Ph.D., M.B.A. Senior Research Scientist and Laboratory Manager Director, Crystallography and Structure Based Drug Design Core Facility Department of Biochemistry and Molecular Biotechnology University of Massachusetts Chan Medical School 364 Plantation St. LRB 970C Worcester MA 01605-4321 Ph: (508) 856-2636 Fax: (508) 856-6215 Email: ala.sha...@umassmed.edu<mailto:ala.sha...@umassmed.edu> website: https://www.umassmed.edu/schifferlab/ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Date: Friday, July 11, 2025 at 7:05 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template You are quite right - 90+120 residues will not fit in a cell of 38.221 38.221 196.300 90.00 90.00 120.00 or 38.221 38.221 149.000 90.00 90.00 120.00 with symmetry P 6 2 2 . So either the cell is wrong, the symmetry is wrong, or the protein is not as you thought.. There is no point trying MR searches till that is sorted.. First suspicious feature. The cell should not change with a different oscillation angle..I think you need to re-examine the data processing carefully and try to understand why the c axis is different.. Then of course spacegroups can be in error If you attach your data processing logs they might provide a clue.. On Fri, 11 Jul 2025 at 10:30, 陈成 <0001179598b916c0-dmarc-requ...@jiscmail.ac.uk<mailto:0001179598b916c0-dmarc-requ...@jiscmail.ac.uk>> 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 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 ________________________________ 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/
