July 2016 - phenixbb - phenix-online.org

How to assign Half occupancy to metal ion in protein crystal
by Sharan Karade 08 Jul '16

08 Jul '16

Dear all, I am refining the protein structure and i want add metal ion in the structure, the site is present in between protein chain and its symmetry mate. when i added metal and refined, it was showing the high B factor and symmetry related metal on the same site. i want to assign the occupancy half and refine but in coot i am unable to do. Is there any method to do this. Thanks in Advance -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Question about restrain of a nonstandard peptide
by Yufan Wu 06 Jul '16

06 Jul '16

Dear Phenix Developers/Users, I have a question regarding how to generate a correct restrain for a whole nonstandard peptide and how do run refinement correctly. The nonstandard peptide in my structure is pepstatin A (IVA Val Val STA Ala STA). I manually put the pepstatin A in the density and generated the cif files for IVA and STA and run the refinement with them. After refinement, the whole pepstatin A explored as pieces, which I guess the program treated the pepstatin A as single amino acids. By the way, I also manual input the “LINK” information in the input pdb file as below, LINK C VAL L 3 N STA L 4 1555 1555 LINK N ALA L 5 C STA L 4 1555 1555 LINK C ALA L 5 N STA L 6 1555 1555 And also, when I use the “Real Space Refine Zone” by clicking two atoms for the whole pepstatin A in coot, it exploded again, although I input the same cif file in coot as well. The data quality is not good (2.9 A with CC1/2=12), thus it is difficult to place amino acid individually to fit the destiny. In the PDB, there are several structures containing the pepstatin A, such as 4TVG, 4AUC. They have the pepatatin A sequence as VVVXAX, but none of them lists the constrains. Would you please help me and let me know how can I continue with refinement? Please let me know if you need more information. Thank you vey much! Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

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Glycan refinement in Phenix.real_space_refine
by Simonas Masiulis 05 Jul '16

05 Jul '16

Hi, I want to refine N-linked glycans into an EM density using Phenix.real_space_refine, but it seems the rings get distorted. Does anybody know how to fix this (e.g., is there a way to provide a .cif file)? Thanks a lot! Simonas

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.cif file created by Jligand for used in phenix.model_vs_data
by luzuok 05 Jul '16

05 Jul '16

Dear all, The protein was covalently linked by my ligand and I used JLigand to generate the link record and the .cif file. This file can be used in Refmac successfully. But the .cif file cannot be recognized by phenix.model_vs_data nor phenix.refine. The program runs with the following message: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 19 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Any suggestions how to do this would be greatly appreciated. Another question is, how can I generate a restraints file for COOT to do real space refinement? The .cif file is imported in COOT, but when I do real space refinement, the link bond still takes apart. Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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iNEXT news
by Anastassis Perrakis 05 Jul '16

05 Jul '16

Dear all, A new access modality has now been open in iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>) "From macromolecular sample to X-ray data collection” This novel access modality, hosted at the EMBL Hamburg and Grenoble Units, will provide transnational access to hands-on assistance for sample characterization and crystallization trials, leading to structural data via X-ray crystallography and/or solution small angle scattering. The users are expected to have a macromolecular sample that has already underwent some initial characterisation, and ideally to have performed initial crystallisation trials with promising results. If users cannot obtain such data in their home laboratory, they can first request a 'Structural Audit' via iNEXT. This modality can provide a report that can be automatically included to this application for pushing the project forward towards obtaining more extensive structural data. Successful "Structural Audits" will be fast-tracked towards extended support via this or other modalities. Please do note, that a small proportion of iNEXT access modalities is also open for non-European users, other than the countries listed in our web site. We also want to remind you that most iNEXT access modalities are now open: Structural Audit (sample mail-in for quality assessment for structural biology studies or SAXS-only characterisation) Mail-in characterization of a macromolecular sample, including stability, oligomeric state, crystallization and SAXS; also NMR and negative stain EM for suitable samples. Enhanced Support (Dedicated expert help for specific structural biology projects) From macromolecular sample to X-ray data collection Hands-on assistance for sample characterization and extensive crystallization trials, leading to structural data via crystallography solution and/or small angle scattering. Cryo-EM sample optimisation Hands-on assistance in optimizing a sample for single particle EM; a good quality preliminary characterization by negative stain is the minimal entry point. Macromolecular interactions Hands-on assistance for quantifying the steady state and transient kinetics underlying macromolecular interactions, by fluorescence methods, MALLS, SPR, ITC, MST High-end Data Collection (For experts: access to high-field NMR, X-ray and high-resolution EM equipment) Synchrotron data Access to synchrotron beamlines for X-ray Crystallography and/or SAXS, for translational research project(s); for single or multiple visits and research groups. High-field NMR Access for experienced NMR-scientists to visit host institutes for acquiring solution or solid state NMR spectra on high-field instruments. High-resolution EM Access to state of the art electron microscopes for single particle, tomography and correlative light and electron microscopy (CLEM). A specific note for synchrotron data applications: projects can request multiple visits for a combination of MX, SAXS, and remote access in multiple sites, and the access can be split in several visits. A “project” should have a scientific theme of translational value, but is not necessarily limited to a specific ’target'. Multiple macromolecules and complexes can be pooled under the same proposal, as long as the research theme can be described in a concise and consolidated manner, with clear statements about availability samples and the reasoning behind specific experiments. "Structural Audit" or "From macromolecular sample to X-ray data collection"? Structural Audit contains basic crystallisation screening, MALLS and SAXS; if you already have such data, we recommend that you proceed to the Enhanced Support. Please do note however, that labs with strong experience in the field, should preferably aim for the High-end Data Collection; these modalities are aiming to help labs new to X-ray studies. Please also note that these are not similar to the old Biostruct-X requests for access to crystallisation facilities only, but are meant to be accessed as a coherent package. Please note that "Structural Audit” review is very rapid and the experiment contains no physical presence, so the application and experiment turnover can be rapid. For questions about X-ray methods please mail me; for NMR and EM related questions please mail Hans H.L.J.Wienk.AT.uu.nl Best regards, Tassos

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