[ccp4bb] screen kit
hello all, is there any screen kit that is highly effective for the crystallization of protein-nucleic acids complexes? deng.
Re: [ccp4bb] PreScission Protease protein sequence
You all might want to be careful about patent infringements, if such exist for prescission. At least don't flaunt it on a BB... JPK On Wed, May 25, 2011 at 9:29 PM, Marc Kvansakul wrote: > Dear BBlers, > > Would the kind donor of the prescission protease plasmid be willing to > share another round? I would love to make this stuff in the lab... > > Best wishes > > Marc > > > > On 26/05/11 12:04 PM, "Lieh Yoon Low" wrote: > >>Dear All, >>Thanks to all who replied me so quickly. In case you do not know, like >>myself until a few hours ago, that this protease is also known as the 3C >>protease from human rhinovirus. Thanks to Dima, the sequence is here if >>anyone is interested: >> >>gpeheflnal irrnchiitt dkgefnllgi ysncavvpth aepgdvvdid grlvrvlkqq >>vltdmndvdt evtvlwldqn ekfrdirrfi pehqqdwhni hlatnvtkfp mlnvevghtv >>pygeinlsgn atcrlykydy ptqpgqcgav lantgniigi hvggngrvgy aaallrkyfa >>eeq >> >>Someone within the bb has already offered to send the expression plasmid >>to me, and I understand that many labs already has it. You just need to >>ask around! >> >>Thanks again >> >>ray > -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] Histogram/Plot of Buried Surface Areas
Dear Crystallographers, is anyone aware of a reference or plot addressing buried surface area (or PISA output values) versus veracity of a complex? I am trying to determine the physiological relevance of a crystallographically-observed assembly, and would love to put my PISA output in the context of verified complexes versus crystal contacts. Thanks, Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] PreScission Protease protein sequence
Dear BBlers, Would the kind donor of the prescission protease plasmid be willing to share another round? I would love to make this stuff in the lab... Best wishes Marc On 26/05/11 12:04 PM, "Lieh Yoon Low" wrote: >Dear All, >Thanks to all who replied me so quickly. In case you do not know, like >myself until a few hours ago, that this protease is also known as the 3C >protease from human rhinovirus. Thanks to Dima, the sequence is here if >anyone is interested: > >gpeheflnal irrnchiitt dkgefnllgi ysncavvpth aepgdvvdid grlvrvlkqq >vltdmndvdt evtvlwldqn ekfrdirrfi pehqqdwhni hlatnvtkfp mlnvevghtv >pygeinlsgn atcrlykydy ptqpgqcgav lantgniigi hvggngrvgy aaallrkyfa >eeq > >Someone within the bb has already offered to send the expression plasmid >to me, and I understand that many labs already has it. You just need to >ask around! > >Thanks again > >ray
Re: [ccp4bb] PreScission Protease protein sequence
Dear All, Thanks to all who replied me so quickly. In case you do not know, like myself until a few hours ago, that this protease is also known as the 3C protease from human rhinovirus. Thanks to Dima, the sequence is here if anyone is interested: gpeheflnal irrnchiitt dkgefnllgi ysncavvpth aepgdvvdid grlvrvlkqq vltdmndvdt evtvlwldqn ekfrdirrfi pehqqdwhni hlatnvtkfp mlnvevghtv pygeinlsgn atcrlykydy ptqpgqcgav lantgniigi hvggngrvgy aaallrkyfa eeq Someone within the bb has already offered to send the expression plasmid to me, and I understand that many labs already has it. You just need to ask around! Thanks again ray > - Original Message - > From: "Lieh Yoon Low" > To: CCP4BB@JISCMAIL.AC.UK > Sent: Wednesday, May 25, 2011 1:36:10 PM GMT -08:00 US/Canada Pacific > Subject: [ccp4bb] PreScission Protease protein sequence > > Dear All, > > I apologize for a non-crystallography question, but does anyone know the > sequence of the PreScission Protease? I would like to make it for use in my > own lab. It is just too expensive to purchase from GE! > > Thanks > > ray > > -- > Michael C. Thompson > > Graduate Student > > Biochemistry & Molecular Biology Division > > Department of Chemistry & Biochemistry > > University of California, Los Angeles > > mi...@chem.ucla.edu
[ccp4bb] Pymol question
Hi everyone, I have two questions: 1- Does anybody know what are the units on the display ruler after you calculate the vaccum electrostatics using pymol? 2- What are the default kT/e values used by pymol? Thank you, Maher
Re: [ccp4bb] Problem running WinCoot
Hey Paul, That totally worked! Thanks for the quick response!!! Terry On 5/25/2011 3:04 PM, Paul Emsley wrote: On 25/05/11 21:20, Terry Lang wrote: Hey Everyone, I am having some problems running Probe Clashes on WinCoot. I am running phenix.refine to obtain the pdb file and then WinCoot for manual building. I have the following installed: WinCoot (6.0.1), probe (2.12.110413) and reduce (3.14.080821) REDUCE_HET_DICT points to a valid location for reduce_wwPDB_het_dict.txt When I ran things originally, I got this error: "BL WARNING:: reduce didnt run ok, so stop here!" Some googling got me to this posting: http://www.proteincrystallography.org/ccp4bb/message14548.html I manually applied the fix. As a result, reduce runs without any apparent error, but returns 1 which causes the probing process to exit. Indeed, I recently had occasion to make this fix in the scheme version. It is not clear to me why there is an exit status of 1 - as you say, reduce seems to work properly. I have also tried modifying generic_objects.py to ignore the error and continue on with the reduced.pdb file that reduce outputted, I end up getting this error: Traceback (most recent call last): File "", line 1, in File "E:\WinCoot\share\coot\python\generic_objects.py", line 236, in probe user_mods_gui(imol_probe, reduce_out_pdb_file) File "E:\WinCoot\share\coot\python\coot_gui.py", line 4399, in user_mods_gui no_adj_buttons = make_no_adj_buttons(flips[1]) File "E:\WinCoot\share\coot\python\coot_gui.py", line 4345, in make_no_adj_buttons chain_id = atom_spec[1] NameError: global name 'atom_spec' is not defined run_generic_script (probe, 0) Comment out this: # show the GUI for USER MODS if using_gui(): user_mods_gui(imol_probe, reduce_out_pdb_file) in WinCoot\share\coot\python\generic_objects.py. Paul. -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3
Re: [ccp4bb] Problem running WinCoot
On 25/05/11 21:20, Terry Lang wrote: Hey Everyone, I am having some problems running Probe Clashes on WinCoot. I am running phenix.refine to obtain the pdb file and then WinCoot for manual building. I have the following installed: WinCoot (6.0.1), probe (2.12.110413) and reduce (3.14.080821) REDUCE_HET_DICT points to a valid location for reduce_wwPDB_het_dict.txt When I ran things originally, I got this error: "BL WARNING:: reduce didnt run ok, so stop here!" Some googling got me to this posting: http://www.proteincrystallography.org/ccp4bb/message14548.html I manually applied the fix. As a result, reduce runs without any apparent error, but returns 1 which causes the probing process to exit. Indeed, I recently had occasion to make this fix in the scheme version. It is not clear to me why there is an exit status of 1 - as you say, reduce seems to work properly. I have also tried modifying generic_objects.py to ignore the error and continue on with the reduced.pdb file that reduce outputted, I end up getting this error: Traceback (most recent call last): File "", line 1, in File "E:\WinCoot\share\coot\python\generic_objects.py", line 236, in probe user_mods_gui(imol_probe, reduce_out_pdb_file) File "E:\WinCoot\share\coot\python\coot_gui.py", line 4399, in user_mods_gui no_adj_buttons = make_no_adj_buttons(flips[1]) File "E:\WinCoot\share\coot\python\coot_gui.py", line 4345, in make_no_adj_buttons chain_id = atom_spec[1] NameError: global name 'atom_spec' is not defined run_generic_script (probe, 0) Comment out this: # show the GUI for USER MODS if using_gui(): user_mods_gui(imol_probe, reduce_out_pdb_file) in WinCoot\share\coot\python\generic_objects.py. Paul.
Re: [ccp4bb] PreScission Protease protein sequence
Hi, This article says it is the Human Rhinovirus HRV3C Protease: https://wasatch.biochem.utah.edu/chris/links/PrescissionProteaseProtocol.doc The genome of this virus is here: http://www.ncbi.nlm.nih.gov/nuccore/156254956 The gene record for the polyprotein is here: http://www.ncbi.nlm.nih.gov/gene/5758809 The poly protein sequence is here: http://www.ncbi.nlm.nih.gov/protein/156254957 Then the 3C protein, ie, the protease is this guy: http://www.ncbi.nlm.nih.gov/protein/156254957?from=1502&to=1684&report=gpwithparts If you blast this sequence in PDB, you will get 43 hits. I suggest you to have a look at some of the structures to decide how to design your construct. This protease shares some characteristics with the TEV protease, for example, Cys protease, having no disulfide bonds but multiple Cys residues, recognizing a fairly hydrophobic sequence. So I guess you may also want to consult the people who were successful with designing and producing TEV protease constructs. My experience with TEV is: 1) a self-cleavable MBP fusion (See TEV FAQ, by Dr. Waugh) works very well, although a non-cleavable MBP fusion also works; 2) do not send the protein to periplasm. Zhijie -- From: "Lieh Yoon Low" Sent: Wednesday, May 25, 2011 4:36 PM To: Subject: [ccp4bb] PreScission Protease protein sequence Dear All, I apologize for a non-crystallography question, but does anyone know the sequence of the PreScission Protease? I would like to make it for use in my own lab. It is just too expensive to purchase from GE! Thanks ray
[ccp4bb] off topic question
Hi, A nuclear receptor is purified only in the presence of strong affinity bound ligand. Is there some method to study and quantitate binding affinities of this protein with other ligands (it is bound to the high affinity ligand after purification)? Attempts to purify in presence of low affinity ligands and subsequent substitution trials were not successful. I therefore seek suggestions from the expert community. Gauri
[ccp4bb] PreScission Protease protein sequence
Dear All, I apologize for a non-crystallography question, but does anyone know the sequence of the PreScission Protease? I would like to make it for use in my own lab. It is just too expensive to purchase from GE! Thanks ray
[ccp4bb] Problem running WinCoot
Hey Everyone, I am having some problems running Probe Clashes on WinCoot. I am running phenix.refine to obtain the pdb file and then WinCoot for manual building. I have the following installed: WinCoot (6.0.1), probe (2.12.110413) and reduce (3.14.080821) REDUCE_HET_DICT points to a valid location for reduce_wwPDB_het_dict.txt When I ran things originally, I got this error: "BL WARNING:: reduce didnt run ok, so stop here!" Some googling got me to this posting: http://www.proteincrystallography.org/ccp4bb/message14548.html I manually applied the fix. As a result, reduce runs without any apparent error, but returns 1 which causes the probing process to exit. I have also tried modifying generic_objects.py to ignore the error and continue on with the reduced.pdb file that reduce outputted, I end up getting this error: Traceback (most recent call last): File "", line 1, in File "E:\WinCoot\share\coot\python\generic_objects.py", line 236, in probe user_mods_gui(imol_probe, reduce_out_pdb_file) File "E:\WinCoot\share\coot\python\coot_gui.py", line 4399, in user_mods_gui no_adj_buttons = make_no_adj_buttons(flips[1]) File "E:\WinCoot\share\coot\python\coot_gui.py", line 4345, in make_no_adj_buttons chain_id = atom_spec[1] NameError: global name 'atom_spec' is not defined run_generic_script (probe, 0) Which I haven't yet attempted to bypass. Has anyone seen this problem? Thoughts on how to improve things? Thanks Terry PS I am committed to getting this running on my Windows environment, so snarky comments about the inferiority of the operating system will be less useful. -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3
Re: [ccp4bb] Software for "Conserved Solvent"
Hi Jacob, On Wed, 2011-05-25 11:58 EDT, Jacob Keller wrote: > Dear Crystallographers, > > does anyone know of a program to compare multiple structures and > identify which solvent molecules (water, ions, etc.) are conserved > between the structures? I guess it would be nice also if it could > identify when, for example, a Cl- in structure A was re-occupied by an > HOH in B, or even some atom in a ligand being replaced by a water. PyMOL's selection routines can allow something like this. To find all waters and ions in one structure that are within 0.5 Angstroms (for example) of the waters and ions in another structure you can type: select conserved_waters, structure1 &! polymer &! organic within 0.5 of structure 2 &! polymer &! organic You can then either save that selection to a file or iterate through it to look at the details: iterate conserved_waters, print chain,resn,resi,name To search for an ion (or ligand atom) that replaces a water you could do: select structure1 & r. hoh within 0.5 of structure1 &! polymer &! r. hoh If you wanted to do this sort of thing on a large set of structures, then it could be scripted in a more user-friendly way. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 http://pldserver1.biochem.queensu.ca/~rlc
[ccp4bb] Software for "Conserved Solvent"
Dear Crystallographers, does anyone know of a program to compare multiple structures and identify which solvent molecules (water, ions, etc.) are conserved between the structures? I guess it would be nice also if it could identify when, for example, a Cl- in structure A was re-occupied by an HOH in B, or even some atom in a ligand being replaced by a water. Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] Position available at Syngenta
Protein Crystallographer Jealott's Hill, Bracknell, Berkshire, UK We are looking for a postdoctoral fellow with a PhD in biochemistry or equivalent who is enthusiastic about working across the range of protein crystallography activities, from protein production to structure refinement of proteins and protein-ligand complexes. The qualified candidate will have a strong background in protein production and crystallisation as well as x-ray data collection, structure refinement and validation. Computational and molecular modelling skills are a plus. Candidates will need to demonstrate flexible teamworking and a tenacious approach to delivering structural solution outputs to projects. Excellent communication skills and the ability to translate structural knowledge to a meaningful output for multidisciplinary project teams are highly desirable qualities for this post. Syngenta is a world-leading agribusiness committed to sustainable agriculture through innovative research and technology. The company is a leader in crop protection, and ranks third in the high-value commercial seeds market. Sales in 2010 were approximately $11 billion. Syngenta employs over 26,000 people in more than 90 countries. Syngenta is listed on the Swiss Stock Exchange (SYNN) and on the New York Stock Exchange (SYT). Jealott's Hill International Research Centre is the largest research and technology site within the company. Further information is available at www.syngenta.com. If you are excited by the prospect of developing your career with a world-leading agribusiness, we would like to hear from you. The post is expected to be for two years. The successful candidate will be employed by SRG and placed at Syngenta, Bracknell. Please visit http://www.srg.co.uk/syngentajobs.aspx to apply online. Informal enquiries can be made to Daniel Kloer (daniel.kl...@syngenta.com).
Re: [ccp4bb] Peptide Crystallization
You could also consider organic solvents (or a mix) for crystallisation trials too. If you scan through the literature you will find that small peptides have in the past been treated as small molecules in terms of crystallization. Once the peptide gets over say 20 amino acids (not the exact number) then the peptides are treated more as small proteins for crystallography. On a side I did just see that the structure of Lysozyme in 50% ethanol was deposited in the PDB (not that lysozyme is a small peptide). Good Luck! Gina -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Buz Barstow Sent: Wednesday, May 25, 2011 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Peptide Crystallization Dear all, I am considering trying to crystallize a small peptide (around 15 amino acids). The peptide is soluble in neutral water or buffer (pH 7.0) until at least 10 mM (13 mg/mL), and adopts a turn conformation when bound to Zn. What are your thoughts on attempting this? If you think that it is worthwhile, what crystallization conditions would you try? I am thinking of a sparse matrix screen using the Hampton Crystal Screen 1 and 2 kits, using hanging drop crystallization in Hampton Vdx trays. Thanks! and all the best, ---Buz Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Peptide Crystallization
I would discourage using pre-made screens on a project outside the norm. The main problems are: Zinc: At mM concentrations will easily crystallize and give false positives in many screens. It will also act as a precipitant for the peptide. The best approach would be to separate the zinc adduct from the non-complexed to avoid heterogeneity. During crystallization to avoid loosing the zinc it might be good to add 50-200mM imidazole with 0.5-10mM zinc. You can either add this to each precipitant solution (best) or to the peptide solution (dangerous as it may all precipitate). Then you can use precipitants except phosphate as it will give false positives avoid EDTA and other strong chelators (but weak chelators like imidazole will be good). If there are specific problems, many from CCP4BB will provide suggestions. Enrico. On Wed, 25 May 2011 14:04:23 +0200, Buz Barstow wrote: Dear all, I am considering trying to crystallize a small peptide (around 15 amino acids). The peptide is soluble in neutral water or buffer (pH 7.0) until at least 10 mM (13 mg/mL), and adopts a turn conformation when bound to Zn. What are your thoughts on attempting this? If you think that it is worthwhile, what crystallization conditions would you try? I am thinking of a sparse matrix screen using the Hampton Crystal Screen 1 and 2 kits, using hanging drop crystallization in Hampton Vdx trays. Thanks! and all the best, ---Buz -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?
Thank you for replies. I understand that real space refinement using maps generated by REFMAC doesn't affect cross validation. I found the documentation of REFMAC about this topic. http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#mapcalc Oops, I should have found this earlier. Thanks again, Keitaro
Re: [ccp4bb] Peptide Crystallization
NMR ... synthesize with a few labeled aa according to taste of local NMR guru. If they cant do a15-aa peptide in a day, let the bb know, it will be entertaining ;-) A. On May 25, 2011, at 14:04, Buz Barstow wrote: Dear all, I am considering trying to crystallize a small peptide (around 15 amino acids). The peptide is soluble in neutral water or buffer (pH 7.0) until at least 10 mM (13 mg/mL), and adopts a turn conformation when bound to Zn. What are your thoughts on attempting this? If you think that it is worthwhile, what crystallization conditions would you try? I am thinking of a sparse matrix screen using the Hampton Crystal Screen 1 and 2 kits, using hanging drop crystallization in Hampton Vdx trays. Thanks! and all the best, ---Buz P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] Peptide Crystallization
Dear all, I am considering trying to crystallize a small peptide (around 15 amino acids). The peptide is soluble in neutral water or buffer (pH 7.0) until at least 10 mM (13 mg/mL), and adopts a turn conformation when bound to Zn. What are your thoughts on attempting this? If you think that it is worthwhile, what crystallization conditions would you try? I am thinking of a sparse matrix screen using the Hampton Crystal Screen 1 and 2 kits, using hanging drop crystallization in Hampton Vdx trays. Thanks! and all the best, ---Buz
Re: [ccp4bb] Ubiquitin E2-E3 co-crystallization
Dear Gett, Maybe you want to start by rephrasing the original question. What you need to know before anything else, is which E2 works together with your new E3, at least in vitro. Crystallizing with a random E2 sounds like a very bad idea - even if that works, why would it be interesting? Needles to say that this is a very difficult project, unless you are a lab with considerable expertise in E2/E3 interactions ... (don't we all love GMAIL addresses for ccp4bb?) A. On May 24, 2011, at 15:48, manjeet mukherjee wrote: Hi all, I am working on a newly identified E3 ubiquitin ligase (RING type). I am interested to co-crystallize it with E2 enzyme. Among the papers reported so far, which are just a few, people have used a mixture of E2s including UbcH1, UbcH5 and UbcH6 for the ubiquitination assays. However, there is no clear evidence on E2 enzyme functions with this E3 ubiquitin ligase in vivo. Can someone suggest how can I choose one particular E2 (among UbcH1/ UbcH5/UbcH6/UncH7...) for co-crystallization studies. It should be noted that all these E2 enzymes have a similar fold, so will it make sense to just randomly choose any one of these E2 enzymes and get started. Also, if someone with experience in this area suggest weather a Ub- E2-E3 complex is stable enough and suitable for ternary complexes. Thanks in advance. -Geet P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] how to remove part of data with bad signal to noise ratio
Dear Dale, For me, a high quality map is a map which clearly shows where the model is correct and where adjustments are needed, e.g. in places where the search model is different from the structure to be solved and in places where the model is missing. This is not the same as a difference in contour level. The most impressive example I have seen was with proTAFI. Here we had 3 molecules in the asymmetric unit. 2 molecules were well-defined, one was somewhat disordered. The prodomain had 91 residues, the catalytic domain 309. The resolution was 2.5Å (optimistic estimate) and the solvent content was 72%. The structure was solved with phaser using a model of the catalytic domain only (~3/4 of the total). The resulting maps clearly showed positive difference density for the complete 2 well-ordered prodomains (92 residues), which could be fitted in one go. I have never seen something like that with crystals with a lower solvent content (say 50% or less). In these cases we would need several cycles of model building and refinement before the complete missing parts could be fitted. Best regards, Herman -Original Message- From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu] Sent: Tuesday, May 24, 2011 6:33 PM To: Schreuder, Herman R&D/DE Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to remove part of data with bad signal to noise ratio On 5/24/2011 2:35 AM, herman.schreu...@sanofi-aventis.com wrote: > Dear Clement, > > In case of a noisy experimental map, you have to do explicit solvent > flattening. However, in case of molecular replacement, if the model > occupies only say 30% of the asymmetric unit, the solvent where there > is no model, will be flattened automatically. You can also view it > like > this: if 70% of the asymmetric unit is featureless solvent, the model > at hand (=flat bulk solvent model), will be very accurate. I never > really tested this, but in the cases where I had a very high solvent > content, I was always surprised by the quality of the electron density > maps. Off If you choose your contour level based on the map rms (often inappropriately called "sigma") the 2Fo-Fc density of a high-solvent-content map will appear stronger even when the absolute quality is the same. All that flat space will cause the overall rms to be low even if the rms calculated over the protein is the same. Dale Tronrud > course, crystals with a high solvent content tend to diffract poorly > and if the solvent is not featureless, this will not work either. > > If you get high Rfree values for a structure with high solvent > content, I would get suspicious and look for extra molecule(s), which > may have been overlooked. If these extra molecule(s) are disordered, > this will off course lead to high Rfree values. > > Best, > Herman > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Clement Angkawidjaja > Sent: Tuesday, May 24, 2011 11:19 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] how to remove part of data with bad signal to > noise ratio > > But you have to do solvent flattening (density modification), which > people often (unintentionally?) skip for structures solved with > molecular replacement. Please correct me if I am wrong. > > Clement > > On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote: > >> This is not my experience. Provided the solvent is featureless, I >> find > >> that a high solvent contents leads to a lower Rfree due to a kind of >> solvent flattening effect. Of course, if a significant part of the >> molecule(s) is/are disordered, this will lead to a degradation of the >> Rfree. >> >> My 2 cents, >> Herman
