What's your twin fraction in each of your anticipated space groups ? That could be the other explanation for your dilemma.
Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/<http://web.me.com/bosch_lab/> On Jan 26, 2011, at 7:56 AM, Kris wrote: Hi everyone, I have a tricky structure that has pseudo-symmetry. Before we publish the structure, we would really appreciate some valuable feedback from experts like yourself. I have recently solved a crystal structure (2.2 Angstrom) made up of a peptide bound to a dimer. If I solve the structure in C2221 (Rfree = 25%), the asu consists of: 1) Dimer A-A' + peptide 1 (on symmetry axis) 2) Dimer B-B' + peptide 2 (on symmetry axis) 3) Dimer C-D + peptide 3 However, if I solve the structure in P21 (Rfree = 28%), the asu consists of: 1) Dimer A-B + peptide 1 2) Dimer C-D + peptide 2 3) Dimer E-F + peptide 3 4) Dimer G-H + peptide 4 Our peptide sequence is almost symmetrical (e.g. LLLGGGRGGGIII) , thus it is possible for it to be on the symmetry axis. However, in order to determine if the peptide really binds in both directions, we decided to synthesise a Se-Met labelled peptide. (We mutated one of the residues that does not interfere with binding into Met.) Recently, we collected 3 SAD data sets (3.0, 3.5, 3.7 Angstrom, 360 degrees each) of the Se-Met labelled peptide bound to the dimer. We processed the data in both P21 and C2221, then generated the anomalous difference map, using the above 2.2 Angstrom solved structure. The results are as follows: P21, 3.0 Angstrom Peptide 1: 2 anomalous signals (sigma level set to 3.0) --> Forward and reverse direction Peptide 2: 2 anomalous signals Peptide 3: 1 anomalous signal --> Forward direction only Peptide 4: 1 anomalous signal --> Forward direction only P21, 3.5 Angstrom Peptide 1: 2 anomalous signals Peptide 2: No anomalous signals Peptide 3: 1 anomalous signal --> Forward direction only Peptide 4: 1 anomalous signal --> Forward direction only P21, 3.7 Angstrom Peptide 1: 2 anomalous signals Peptide 2: 1 anomalous signals --> Forward direction only Peptide 3: 1 anomalous signal --> Forward direction only Peptide 4: 2 anomalous signals C2221, 3.0 Angstrom Peptide 1: 1 anomalous signal --> Forward direction only Peptide 2 & 3: (on symmetry axis) C2221, 3.5 Angstrom Peptide 1: 1 anomalous signal --> Forward direction only Peptide 2 & 3: (on symmetry axis) C2221, 3.7 Angstrom Peptide 1: 2 anomalous signals Peptide 2 & 3: (on symmetry axis) As the results do not consistently show that the peptide binds in both directions, we are now in a dilemma. How should we publish this structure and in which space group, since the structures in both space group refine very well with good statistics? Thank you in advance for all your suggestions and advice. Yours sincerely, Kris
