- phenixbb - phenix-online.org

Re: [phenixbb] Anomalous or not?
by Ryan Spencer 10 Jul '14

10 Jul '14

The question then becomes how do you know the bromine is in the crystal? Is it covalent on the protein? Is it covalent on the ligand? How do you know if the ligand is in the structure? We have seen rapid crystal degredation with Br at its edge. Do you see the resolution significantly degrade after a few frames? I don't think it's a processing issue with xds or with phenix. Ryan -------- Original message -------- From: CPMAS Chen <cpmasmit(a)gmail.com> Date: 07/10/2014 9:52 AM (GMT-08:00) To: Ryan Spencer <rspencer(a)uci.edu> Cc: Francis Reyes <Francis.Reyes(a)colorado.edu>,phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Anomalous or not? Well, let me make this clear. 1. I am using Br anomalous signal to identify the potentially bound ligand. 2. I do shoot the crystals at 0.92A. 3. the different crystals have different resolution, but anomalous signal was weak as reported by autoxds. Charles On Thu, Jul 10, 2014 at 12:25 PM, Ryan Spencer <rspencer(a)uci.edu> wrote: So I assume you were not able to shoot the crystal at ~0.92 A at SSRL or are the crystals sensitive? If you were limited to the single wavelength beam which is around 1A you’re dealing with a really low f” of 0.5322. There have been crystals solved with Sulfur using an in-house Cu sources (takes a lot of merged sets and anomalous is stronger at certain crystal angles) which gives about the same anomalous scattering as Br. Is the bromine covalent or is it soaked ion? Alternatives – soak with potassium iodide and get a dataset from an in-house source (iodine f” 6.6 at 1.54), or at least the anomalous locations. You may get a partial model to use for replacement at that point. Did each processed dataset have the same level of anomalous signal when processed individually? Ryan From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of CPMAS Chen Sent: Thursday, July 10, 2014 8:55 AM To: Francis Reyes Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Anomalous or not? Francis, My anomalous plot for Br is more like your Cobalt 1 site less redundancy. Ryan, As my Br anomalous signals are weak, I merged signals from multiple crystals. Meanwhile I am looking into the detail about the autoxds processing as suggested by Tim. Thanks, On Thu, Jul 10, 2014 at 10:02 AM, Francis Reyes <Francis.Reyes(a)colorado.edu> wrote: In addition to Tim's comments above, using loggraph to see the anomalous CC plot from scala is a good qualitative indicator of whether you have anomalous signal.. Some data points for what reasonable plots (and their corresponding XDS SigANO's) look like: https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf F On Jul 10, 2014, at 9:03 AM, CPMAS Chen <cpmasmit(a)gmail.com> wrote: > > Which result should I trust? By the way, how can I view/display the ***.anamplot file, which is apparently xmgr format file, but I can not display in CCP4i. > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ****************************************************** -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Postdoctoral Position in Membrane Protein Structural Biology
by Noinaj, Nicholas (NIH/NIDDK) [E] 07 Jul '14

07 Jul '14

Two postdoctoral positions in structural biology are available starting in August in my new laboratory within the Biological Sciences department at Purdue University. As part of the Markey Center for Structural Biology, my lab will integrate electron microscopy and X-ray crystallography with biochemical methods to study the biogenesis of beta-barrel membrane proteins in Gram-negative bacteria with a focus on eventual therapeutic development against pathogenic strains of bacteria (See Noinaj et al., Structure (in press, 2014), Nature, 501:385-390 (2013), and Nature, 483:53-58 (2012)). The Markey Center for Structural Biology at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, receptors, signaling proteins and enzymes in addition to methods development in crystallography, NMR and electron microscopy. My lab is located within the Hockmeyer Hall of Structural Biology which boasts state-of-the-art shared resources including a Titan Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, Rigaku X-ray generators and detectors, and other advanced instrumentation available at the Bindley Bioscience Center, the Birck Nanotechnology Center, and the new Center for Drug Discovery. In addition, Purdue is in close proximity to the Advanced Photon Source at Argonne National Lab for convenient access to synchrotron data collection. The successful candidate(s) should be highly motivated, have strong written and communication skills, have (or expect) a recent PhD in structural biology, biophysics, biochemistry, or other related field of study and have previous experience in working with membrane proteins and/or X-ray crystallography or electron microscopy. Applicants should send a CV, names of three referees and a statement describing your interests and relevant work experience to Nicholas Noinaj at nicholas.noinaj(a)gmail.com<mailto:[email protected]>. Nicholas Noinaj Purdue University Department of Biological Sciences 333 Hockmeyer Hall 915 W State St West Lafayette, IN 47907

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Autobuiold from polyalanine model
by Chieh Yin 07 Jul '14

07 Jul '14

Dear Phenix Users, I am doing the molecular replacement to solve a membrane protein structure(transmembrane and soluble domain). The structure of the soluble domain is known, 200AAs. And there is a homology structure of transmembrane domain, 350AAs. I used the polyalanine model of the homologous model of transmembrane domain to do the first search. I got a solution with TFZ 16. Then used the partial solution to do the second search with the soluble domain as the model.I also got a solution with TFZ about 15. The density map showed I got the right solution. And the simple rigid body refinement yielded a Rfactor/Rfree 0.29/0.32. Then I used the polyalanine model and the soluble domain as the starting model to do the phenix autobuild. But it seemed that Autobuild didn't replace the alanine with the real sequence AAs. I tried to set the rebuild in place to false but I still got the same result. The Autobuild even didn't change any amino aside reside from the starting model. I hope you could figure out the problem for me. Thank you in advance! Best regards, Jie

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distinguish between metals
by Aleksandar Bijelic 01 Jul '14

01 Jul '14

Dear phenix developers and users, I wanted to ask if there is a possibility to considerably distinguish betwenn two/three metals. I crystallized an iron-binding protein (transferrin in apo form) with a Ru- and Ga-compound. I see density in the metal-binding site which should come from the Ru/Ga metal since crystallization was done with the apo-form, but nevertheless I need to prove this. The wavelength of the X-ray was 1.02 Angstrom and the respective f''and f' values for the metals are +1.66e/+0.30e (Fe), +1.62/-0.5 (Ru) and +2.95/-0.76 (Ga). Is it possible to distinguish between Ru/Ga and Fe and thus to prove that Fe was not bound? The resolution is moderate with 3.1 angstrom and all metals are able to exhibit the same coordination geometry, thus you cannot distinguish according to the geometry. Unfortunately, I was also not able to measure the crystal with multiple wavelenghts because the crystals were very fragile. I hope you can help me and give me some advice. Thank you in advance. Best Regards, Aleks -- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 1090 Wien Tel: +43 1 4277 52536 e-Mail:[email protected]

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mailing list
by Aleksandar Bijelic 01 Jul '14

01 Jul '14

aleksandar.bijeli(a)univie.ac.at -- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 1090 Wien Tel: +43 1 4277 52536 e-Mail:[email protected]

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select sphere syntax
by Tanner, John J. 28 Jun '14

28 Jun '14

Is there a way to select a sphere of residues in the phenix.superpose_pdbs command, analogous to the "around" syntax in cns? I tried "within" and "around" in phenix.superpose_pdbs but got "Atom selection syntax error". Thanks. Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tannerjj(a)missouri.edu<mailto:[email protected]> phone: 573-884-1280 fax: 573-882-2754 http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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Coot DNA names
by Bradley Hintze 27 Jun '14

27 Jun '14

Hey Folks, Does anybody know a quick way to convert DNA atom names back to PDB standard after coot modifies them to match the ccp4 dictionary? Thanks -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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quick R-value calculation
by Patrick Loll 27 Jun '14

27 Jun '14

I have a structure pulled from the PDB that contains a gnarly, complex ligand, for which I don't have a library. I just want to do a quick R-value calculation +/- ligand, and I don't want to go to the trouble of building and testing a library just for this purpose. Is there some way to induce phenix.refine or phenix.model_vs_data to do the R-value calculation even if it doesn't recognize the nonbonded energy type symbols? Thanks for any tips. Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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seeking help about running SCALEPACK2mtz
by chen c 26 Jun '14

26 Jun '14

Dear PHENIXBBers: I'e got a problem about data processing when running SCALEPACK2mtz. Hope you can give me some advice on that. Here's my problem: I have an .sca file processed by HKL2000 about 4 years ago, I just ran the Scalepack2mtz program in order to transform it into .mtz file. However, the program keeps running. To ensure that the Scalepack2mtz program is ok, I use another .sca file for verification and it turns out that this file for verification is successfully transformed into .mtz file within seconds. I checked the .log file, the program keeps running when there are the following messeages: "Mean acentric moments I from input data: <I^2>/^2 = 2.360 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 9.187 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 52.348 (Expected value = 24.000, Perfect Twin = 7.500) Mean acentric moments I from anisotropically corrected data: <I^2>/^2 = 3.121 (Expected = 2.000, Perfect Twin = 1.500) <I^3>/^3 = 12.788 (Expected value = 6.000, Perfect Twin = 3.000) <I^4>/^4 = 57.952 (Expected value = 24.000, Perfect Twin = 7.500) " does this means that the .sca file isn't processed properly? I also checked the scale.log file, and there are the following messages: " Shell Summary of observation redundancies: Lower Upper % of reflections with given No. of observations limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 >19 total 50.00 5.60 5.9 6.1 18.0 15.1 26.9 19.7 8.3 0.0 0.0 0.0 94.1 5.60 4.45 7.9 9.4 13.0 12.9 23.2 27.5 6.1 0.0 0.0 0.0 92.1 4.45 3.88 19.2 5.6 13.3 13.5 20.4 21.9 6.0 0.0 0.0 0.0 80.8 3.88 3.53 31.9 6.5 11.6 11.3 14.9 17.9 5.8 0.0 0.0 0.0 68.1 3.53 3.28 2.4 4.7 11.3 15.3 23.5 34.1 8.7 0.0 0.0 0.0 97.6 3.28 3.08 0.2 3.6 7.0 15.4 23.7 40.1 9.9 0.0 0.0 0.0 99.8 3.08 2.93 0.4 4.4 8.7 16.8 21.1 41.3 7.2 0.0 0.0 0.0 99.6 2.93 2.80 4.2 8.0 12.7 15.2 20.3 33.7 6.0 0.0 0.0 0.0 95.8 2.80 2.69 15.4 9.1 14.0 13.8 19.2 25.2 3.3 0.0 0.0 0.0 84.6 2.69 2.60 31.6 16.2 11.7 14.2 13.7 10.6 2.0 0.0 0.0 0.0 68.4 All hkl 11.8 7.3 12.2 14.4 20.8 27.1 6.4 0.0 0.0 0.0 88.2 " This clearly indicates an ice ring problem in the data-collection process. However, the ice ring problem shouldn't have caused the error during the .sca to .mtz process. In fact, I have use it for structure-solvement, and currently the two R factor is around 30%. However, the large deviation of <I^3>/^3 or <I^4>/^4 do means something wrong. Would you tell me what exact mistakes did I make? Can I use this .sca file for subsequent structure solving and refinement? Great thanks for your help! best regards chen

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Anisotropic B-factor restraints
by Elke De Zitter 26 Jun '14

26 Jun '14

Dear All I'm refining a protein structure with a resolution of 1.25 A, using Phenix GUI version 1.9. I am refining the B-factors for the protein atoms anisotropic and those for the water molecules isotropic. How can I restrain the anisotropic B-factors so that bonded atoms have similar ellipsoids (like the SIMU and DELU commands in Shelx making the atoms moving similarly in direction and amount)? Thanks Elke Elke De Zitter PhD student, KU Leuven Biochemistry, Molecular and Structural Biology Celestijnenlaan 200f - bus 2404, 3001 Leuven Room 00.84, +32 16 3 26530

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