P3x 2 1 and P3x 1 2 are different. It is worth testing both in data reduction and MR.
Yong From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of 陈成 Sent: Friday, July 11, 2025 11:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template I guess you mean P32 2 1 as you mentioned P32 1 2. The data sets collected using 0. 2 degree oscilliation angle in the second time is better. I had tried indexing in P321 point group and check the option "all possible in same pointgroup" when I guess you mean P32 2 1 as you mentioned P32 1 2. The data sets collected using 0.2 degree oscilliation angle in the second time is better. I had tried indexing in P321 point group and check the option "all possible in same pointgroup" when running MR (ccp4 phaser mr & phenix.mr). The resolution is 1.8 angstrom. Phenix.hyss analysis is also tried and no anomalous signal is suggested. chen Cheng Chen, Associate Professor School 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："Weiss, Manfred" <manfred.we...@helmholtz-berlin.de<mailto:manfred.we...@helmholtz-berlin.de>> 发送日期：2025-07-11 18:23:39 收件人："陈成" <chengc...@tju.edu.cn<mailto:chengc...@tju.edu.cn>> 主题：Re: Re:Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template This is really weird, indeed. Have you also tried P32 1 2? Both P32 2 1 and P32 1 2 are subgroups of P62 2 2, so you should try both of them. What is the resolution of your data set(s)? Is there any indication of anomalous scattering in your data? Which programs do you use for processing? I also had a look at the structure of calprotectin. It seems that the monomer is pretty flexible. Could it be that you observe a different dimer than the one published? Best, Manfred ________________________________ From: 陈成 <chengc...@tju.edu.cn<mailto:chengc...@tju.edu.cn>> Sent: Friday, July 11, 2025 12:04 PM To: Weiss, Manfred Subject: Re:Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template Dear Manfred, So glad to receive your advice~ For the buches of data sets collected using 0.5 degree oscilliation angle, different P6x 2 2 subgroups is indicated. So I tried the indexing in all possible spacegroups including P 1, P 2/P 21, P 3/P 3x (x: 1 to 2), P 6 2 2 and P 6x 2 2 (x: 1 to 5) and then run MR with protein complex, either single protein or its truncated form as search template, which all failed. As for the data sets collected using 0.2 degree oscillation angle, only P 62 2 2 spage group is indicated since systematic absence is clearly revealed. Twinning is not indicated by xtriage analysis. Despite this, I also tried indexing in P 3 2 1 group and run MR as well. Still, no solution is achieved. Really weird.. Chen Cheng Chen, Associate Professor School 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："Weiss, Manfred" <manfred.we...@helmholtz-berlin.de<mailto:manfred.we...@helmholtz-berlin.de>> 发送日期：2025-07-11 17:48:14 收件人："陈成" <chengc...@tju.edu.cn<mailto:chengc...@tju.edu.cn>> 主题：Re: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template Dear Chen, trigonal and hexagonal space groups are notorious for twinning. Is there any indication for that? CHeck the Pointless output. In particular if the asymmetric unit volume is too small to accomodate the complex, twinning seems highly likely. You indicate P622. Could it be P6x22 with x being 1, 2, 3, 4 or 5? Best regards Manfred ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of 陈成 <0001179598b916c0-dmarc-requ...@jiscmail.ac.uk<mailto:0001179598b916c0-dmarc-requ...@jiscmail.ac.uk>> Sent: Friday, July 11, 2025 11:04 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] smaller cell volume for accommodating protein complex & no MR solution even very similar template 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<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!A_kSX19cfVk!DZbTUixcaR2meDh9yu8QdWJBuRU14hyHwWhFFlmD1ulf6k-GKa-zSpe4doYoVv8PKKIFvprds5_v59F7ZzuHytuTF4Gp4o5J00DWQQ$> ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. 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