Deat CCP4ers, In relation to this topic, I'd like to mention that SF4 has replaced FS4 as the Fe4S4 monomer in the CCP4 monomer library.
However, the dictionary values for bond lengths and angles are not correct, and this is especially noticeable when the dictionary is used in a high-resolution refinement (e.g., 1.05 A). In particular, the Fe-S-Fe angles are all set to 90 degrees, when in fact some are smaller and others are larger. This introduces a bias in the final rms angle deviation values. Fe4S4 is a distorted cubane, not a perfect cube. Best regards, Pedro Matias Em 13-10-2014 12:09, "Oliver Smart" escreveu: > Stephen, > > Robbie advice is 100% correct. Be careful about the naming of the sulphur > atoms (is S1 opposite S4 or next to it). I recall that the distributed CCP4 > dictionaries have different atom naming than the PDB chemical components > dictionary. If this is the problem is that the naming is different this > should result > in large restraint violations that should be appear in the REFMAC output > (others can tell you where). > > In general diffraction from Fe S clusters is so strong that the atom > positions > are pretty much determined from the electron density. But in case it helps > I did some work data mining restraints for Fe2S2 and Fe4S4 from CSD > structures (this has to be done manually). Please find attached the > resulting FES.cif and SF4.cif restraint dictionaries (distributed with > BUSTER). > > Good luck, > > Oliver > ------------------- > Dr Oliver Smart > Director SmartSci Limited http://www.smartsci.uk/ > & Consultant Global Phasing Ltd http://www.globalphasing.com/ > > on 10/10/14 5:33 PM, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > >> Dear Stephen, >> >> The dictionary is very specific about atom names. If you have them swapped >> (as many PDB entries do). The angle and chiral volume restraints will > wreck >> your cluster. You also need to make sure to provide LINK records to attach >> the cluster to the surrounding cysteines. >> >> HTH, >> Robbie >> >> Sent from my Windows Phone >> ________________________________ >> Van: <Stephen Carr> >> Verzonden: 10-10-2014 18:07 >> Aan: CCP4BB@JISCMAIL.AC.UK >> Onderwerp: [ccp4bb] Refinement of Iron-sulphur clusters >> >> Dear CCP4 BBers, >> >> I am currently refining a model of a protein containing three iron sulphur >> clusters using Refmac (v5.8.0078) and am getting some unusual results. > One >> of the clusters (3fe 4s) seems to behave resonably and the refined > electron >> density looks very nice. The atoms in the others clusters (4Fe4S and >> 4Fe3S), however, migrate towards the centre of the cluster producing Fo-Fc >> difference maps with strong negative density at the centre surrounded by >> blobs of positive density where the atoms should be. >> >> I have checkedthe refmac dictionaries and there are entries for each of > the >> clusters, so I shouldn't have to explicitly include a cif file for the >> clusters as an input right? In fact, when I did try to include a > dictionary >> file for one of the clusters refmac gave a warning message in the log > about >> duplicate monomers dictionaries and it made no difference to the >> refinement/maps anyway. >> >> On checking the refmac log file there is no specific mention that there > are >> hetero-groups in the pdb file and no explicit mention that it is using any >> dictionaries during the refinement. How can I tell if refmac is >> reading/using the dictionaries? Also bonds within the clusters are > flagged >> up as outliers and deviating by more than 10 sigma from ideal suggesting >> that they are not getting read? >> >> I realise that something chemically odd could be going on at the centres, >> but if I omit them from the model and calculate maps very strong density >> comes back around where the atoms sat before refinement, so I am pretty >> confident that they are in the right place to start with. >> >> Any help with this problem would be greatly appreciated, I'm sure there is >> something obvious that I am missing but can't see what that is at the >> moment. It is particularly confusing since one cluster apparently behaves >> while the others do not. I could, of course, try phenix or buster, but I >> would like to get to the bottom of the problem with refmac if possible. >> >> Thanks very much in advance, >> >> Steve >> >> Dr Stephen Carr >> Research Complex at Harwell (RCaH) >> Rutherford Appleton Laboratory >> Harwell Oxford >> Didcot >> Oxon OX11 0FA >> United Kingdom >> Email stephen.c...@rc-harwell.ac.uk >> tel 01235 567717 >> This email 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 authorized 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 >> this email. >> >> Any views or opinions presented are solely those of the author and do not >> necessarily represent those of the Research Complex at Harwell. >> >> There is no guarantee that this email 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. >> >> We use an electronic filing system. Please send electronic versions of >> documents, unless paper is specifically requested. >> >> This email may have a protective marking, for an explanation, please see: >> >> > http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm >> . >> >> >> -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___________________________________ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Universidade Nova de Lisboa Av. da República - EAN 2780-157 Oeiras PORTUGAL
