Re: [ccp4bb] A strange case of MR
Dear Collins and all, Thanks for the reply. Please find the following pdb header. For your information, this is after refmac5 with twin-refinement option selected. This is the best R values that I'm getting. Cutting resolution does not help much in getting the Rs down... HEADERSWISS-MODEL SERVER (pa-JAN-g) COMPNDSS-MODEL REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.96 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 91.56 REMARK 3 NUMBER OF REFLECTIONS : 27851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.42077 REMARK 3 R VALUE(WORKING SET) : 0.42170 REMARK 3 FREE R VALUE : 0.40609 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.4 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH :1.522 REMARK 3 BIN RESOLUTION RANGE LOW:1.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :82.44 REMARK 3 BIN R VALUE (WORKING SET) :0.529 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE:0.622 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.096 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3B11 (A**2) : 8.45 REMARK 3B22 (A**2) : -12.86 REMARK 3B33 (A**2) : 4.41 REMARK 3B12 (A**2) : 0.51 REMARK 3B13 (A**2) :-1.32 REMARK 3B23 (A**2) :-8.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE(A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.812 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUESCOUNTRMSWEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS(A): 1016 ; 0.008 ; 0.022 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1382 ; 1.482 ; 1.974 REMARK 3 TORSION ANGLES, PERIOD 1(DEGREES): 122 ; 9.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2(DEGREES):46 ;33.363 ;26.087 REMARK 3 TORSION ANGLES, PERIOD 3(DEGREES): 176 ;21.472 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4(DEGREES): 2 ;13.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 144 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 774 ; 0.007 ; 0.022 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMSWEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 624 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1020 ; 1.686 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 392 ; 1.691 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 362 ; 2.734 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1016 ; 0.952 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS :4 REMARK 3 TWIN DOMAIN :1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.307 REMARK 3 TWIN DOMAIN :2 REMARK 3 TWIN OPERATOR : -H, K, -K-L REMARK 3 TWIN FRACTION : 0.191 REMARK 3 TWIN DOMAIN :3 REMARK 3 TWIN OPERATOR : -H, -K, K+L REMARK 3 TWIN FRACTION : 0.198 REMARK 3 TWIN DOMAIN :4 REMARK 3 TWIN OPERATOR : H, -K, -L REMARK 3 TWIN FRACTION : 0.304 REMARK 3 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 REMARK 3 BULK SOLVENT MODELLING.
Re: [ccp4bb] [PyMOL] Label N-Glycosilation with Pymol
On Jul 19, 2010, at 12:29 PM, José Ignacio Sánchez Gallego wrote: Hi everybody, I have to make a 3D structure of my protein, I mutated some aminoacids in order to add some N-linked glycans, does anyone know is it possible to show the glycosilation on the surface of the 3D structure?? It would be a nice picture. Thanks in advance, Greetings Hi José, You can use GlyProt to *model* your glycan chains: http://www.glycosciences.de/modeling/glyprot/php/main.php HTH, Luca Luca Jovine, Ph.D. Group Leader EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
Re: [ccp4bb] Cys-Lysine Side chain Interaction
Hello John, We had just such an issue a year or so ago and I posed the same question to the BB. The density that I observed, and the CCP4bb discussion, can be found at: http://labs.hwi.buffalo.edu/gulick/cyslys.html http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg06092.html I was advised to try metals and a variety of oxidation states for the Cysteine. None of which refined satisfactorily. Ultimately, I believe that what we captured was a thiocarbamate or a thiouronium. We modeled the link as such, and have published the density and our best efforts at modeling this in Shah, M. B., Ingram-Smith, C., Cooper, L. L., Qu, J., Meng, Y., Smith, K. S., and Gulick, A. M. (2009) The 2.1A crystal structure of an Acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl binding pocket for small branched acyl substrates. Proteins 77, 685-698. The Deposited PDB is 3ETC. The paper also describes a few references for chemical precedent. Good luck. Andrew -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 7/16/10 4:00 PM, John R. Horton jrho...@emory.edu wrote: Hello! I am working on a structure that has continuous density from a Lys Nz atom to a Cys Sg; these are ~2.9A from each other. I would consider this a H-bond; however, the 2fo-fc density does not run straight from atom to atom in this 1.9A structure. At an apx right angle, with the line joining these two atoms being the hypotenuse, there is aspherical fo-fc density ~2.1A from the Cys Sg and ~1.7A from the Lys Nz as if another atom sits between these two atoms. The modeled side chains fit the density very well. No other atoms are close by to be ligands so I ruled out an ion. I'd appreciate any thoughts any of you may have...thanks! John Horton Emory University
[ccp4bb] Need suggestion on classification of a protease
Dear Friends, We are doing research on membrane protease. We need to know to how to classify the protease in invitro and insilico levels. Is there is any advanced techniques or methods available, to classify the protease in insilico level? Please give suggestions on this. Waiting for your valuable suggestions. Thank you. With Regards, Gowriishankar R
Re: [ccp4bb] Need suggestion on classification of a protease
Hi, If you do not know anything about peptidase (protease) classification, I'd suggest you have a look first at the Merops peptidase data base: http://merops.sanger.ac.uk/ Will tell you what (type of) classes there are, for example (and based on what). Fred. Gowriishankar Raju wrote: Dear Friends, We are doing research on membrane protease. We need to know to how to classify the protease in invitro and insilico levels. Is there is any advanced techniques or methods available, to classify the protease in insilico level? Please give suggestions on this. Waiting for your valuable suggestions. Thank you. With Regards, Gowriishankar R
Re: [ccp4bb] A strange case of MR
I would be careful with Rfactors at the early stages of refinement, especially in the presence of twinning (apparent or real). You can see weird behaviour of Rfactors in this presentation: www.ysbl.york.ac.uk/refmac/Presentations/Refmac_Erice_workshop.ppt, slides 18-20. In short if you have perfect twinning (you seem to have perfect twinning along one axis, the second axis seems to be ghost) and you have modelled twinning then random R-factor could be as low as 40%. I.e. even if your Rfactor after refinement is around 40 you cannot be sure that you have solved the structure. Best strategy would be to analyse electron density very carefully. Can you see some new features that are not in the model? What happens if you remove several residues and refine? Do they come back. If you want you can send your data and I can try to analyse here to see what is going on regards Garib On 19 Jul 2010, at 08:41, 孙庆祥 wrote: Dear Collins and all, Thanks for the reply. Please find the following pdb header. For your information, this is after refmac5 with twin-refinement option selected. This is the best R values that I'm getting. Cutting resolution does not help much in getting the Rs down... HEADERSWISS-MODEL SERVER (pa-JAN-g) COMPNDSS-MODEL REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.96 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 91.56 REMARK 3 NUMBER OF REFLECTIONS : 27851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.42077 REMARK 3 R VALUE(WORKING SET) : 0.42170 REMARK 3 FREE R VALUE : 0.40609 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.4 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH :1.522 REMARK 3 BIN RESOLUTION RANGE LOW:1.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :82.44 REMARK 3 BIN R VALUE (WORKING SET) :0.529 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE:0.622 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.096 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3B11 (A**2) : 8.45 REMARK 3B22 (A**2) : -12.86 REMARK 3B33 (A**2) : 4.41 REMARK 3B12 (A**2) : 0.51 REMARK 3B13 (A**2) :-1.32 REMARK 3B23 (A**2) :-8.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE(A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.812 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUESCOUNTRMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS(A): 1016 ; 0.008 ; 0.022 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1382 ; 1.482 ; 1.974 REMARK 3 TORSION ANGLES, PERIOD 1(DEGREES): 122 ; 9.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2(DEGREES):46 ;33.363 ; 26.087 REMARK 3 TORSION ANGLES, PERIOD 3(DEGREES): 176 ;21.472 ; 15.000 REMARK 3 TORSION ANGLES, PERIOD 4(DEGREES): 2 ;13.956 ; 15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 144 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 774 ; 0.007 ; 0.022 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 624 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1020 ; 1.686 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 392 ; 1.691 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 362 ; 2.734 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC
Re: [ccp4bb] Postdoctoral position in Houston
Bumping this topic again. Thanks On Tue, Jul 6, 2010 at 9:31 AM, RaDaniel Christian 성준 renderea...@gmail.com wrote: I just want to bump this message up once more. On Thu, Jun 24, 2010 at 6:21 PM, RaDaniel Christian 성준 renderea...@gmail.com wrote: Dear all, A position has become available for a Post-doctoral Refsearch Fellow in the Department of Pharmacology, at Baylor College of Medicine in Houston. The focus of our work is on structural and biochemical characterization of Serine/Threonine protein kinases. The successful candidate will be involved in the complete process of the project, solving the structure of proteins, as well as biochemically characterizing them. The ideal applicant will have a PhD in a biological science, or the equivalent in professional qualifications and experience, and have experience in molecular cloning, protein purification and x-ray crystallography. The laboratory is located in Texas Medical Center campus which provides an excellent environment for academia and research. The lab is well-equipped including robotics to facilitate overproduction and crystallization of proteins and has access to the Berkeley ALS beamline in the framework of the molecular biology consortium. Interested candidates must send three references and a resume to: d...@bcm.edu With kind regards, Daniel Ra -- Daniel Ra - Research Associate Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax) -- Stop the ACTA. Row, row; fight the power! http://www.eff.org/ Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax) -- Stop the ACTA. Row, row; fight the power! http://www.eff.org/ Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax)
Re: [ccp4bb] A strange case of MR
Hi, This is a case of small protein packed in P1. One question may be raised if you have all molecules added to your model? Based on the cell constants and the information of ~60 residues you provided, the solvent content is ~70%, which is not that normal for a small unit cell (18 Å or so), although the Matthews Coefficient calculation may be less accurate. I would check the solvent region! With 4 moles in this P1 cell, the solvent content could be ~36%, which is very normal for small-mol in small cell. If it is true (2 mols in P1) to have such a high solvent content, a Babinet scaling in Refmac may help lower Rs. Also, the Rfree of the highest resolution shell is 60%, which means you may need rethink about the resolution cutoff. According to Wilson's statistics (1950), it is problematic in this model. Can also you show the statistics when data was processed in P2/P21, though I do not think P1 refinement should be the cause of such high Rs. Best luck! Lijun On Jul 19, 2010, at 12:41 AM, 孙庆祥 wrote: Dear Collins and all, Thanks for the reply. Please find the following pdb header. For your information, this is after refmac5 with twin-refinement option selected. This is the best R values that I'm getting. Cutting resolution does not help much in getting the Rs down... HEADERSWISS-MODEL SERVER (pa-JAN-g) COMPNDSS-MODEL REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.96 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 91.56 REMARK 3 NUMBER OF REFLECTIONS : 27851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.42077 REMARK 3 R VALUE(WORKING SET) : 0.42170 REMARK 3 FREE R VALUE : 0.40609 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.4 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH :1.522 REMARK 3 BIN RESOLUTION RANGE LOW:1.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :82.44 REMARK 3 BIN R VALUE (WORKING SET) :0.529 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE:0.622 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.096 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3B11 (A**2) : 8.45 REMARK 3B22 (A**2) : -12.86 REMARK 3B33 (A**2) : 4.41 REMARK 3B12 (A**2) : 0.51 REMARK 3B13 (A**2) :-1.32 REMARK 3B23 (A**2) :-8.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE(A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.812 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUESCOUNTRMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS(A): 1016 ; 0.008 ; 0.022 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1382 ; 1.482 ; 1.974 REMARK 3 TORSION ANGLES, PERIOD 1(DEGREES): 122 ; 9.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2(DEGREES):46 ;33.363 ; 26.087 REMARK 3 TORSION ANGLES, PERIOD 3(DEGREES): 176 ;21.472 ; 15.000 REMARK 3 TORSION ANGLES, PERIOD 4(DEGREES): 2 ;13.956 ; 15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 144 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 774 ; 0.007 ; 0.022 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 624 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1020 ; 1.686 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 392 ; 1.691 ; 3.000 REMARK
[ccp4bb] PhD Fellowship at the University of Copenhagen: Elucidating the structure and mechanism of proton coupled peptide transporters
General announcement and how to apply: http://www.farma.ku.dk/index.php?id=8450 (bottom of page) Project description: http://www.farma.ku.dk/index.php/Project-6/8456/0/ Deadline for applications: *Monday 30 August 2010 at 12 o'clock noon*. About the group: http://www.farma.ku.dk/BR/ Please contact me if you wish further information. Best regards Osman -- Osman Mirza, Associate Professor PhD Department of Medicinal Chemistry Faculty of Pharmaceutical Sciences University of Copenhagen Universitetsparken 2, DK-2100 Denmark Phone: +45 3533 6175 Fax: +45 3533 6040 E-mail: o...@farma.ku.dk/mirzos...@gmail.com
Re: [ccp4bb] A strange case of MR
Hi, Collins, Thanks for the valuable comments. I tried refineing using 2.0A cutoff, but the problem persists. (No Molrep solution is found with R less than 0.7, ). Could you please show me how can I indentify and eliminate the catastrophic error that I'm having with the data? Regards, At 2010-07-19 19:48:35，Collins, Edward J edward_coll...@med.unc.edu wrote: Right. So, you have a good map (not perfect since your CC in fo-fc map is in 80% range- should be in 90%s, but lousy overall statistics. What do the R factors/Rfree look like as a function of resolution? Later in this output file, there are those statistics after each cycle. I just want to know if you have a good R factor and Rfree at low resolution but really bad at high resolution? It is possible, based on the postrefine statistics that you chose to use all of your data, but there was really only good data to about 2.0 angstroms. Depending on how bad the statistics are at high resolution, you could get this bad of an Rfree, but that would be strange. At least, I have never seen the Rfactor at 40% in such a case. high 30% would be more likely. The one bin showed in this file is for the highest resolution (50%) which is pretty bad. If you make your resolution cutoff 20-2.0 angstroms and run for a few cycles, you would see if this is a function of resolution. If those statistics look similar (that is, the low resolution R factor and Rfree are bad too), you have a catastrophic error in your data somewhere. It could be pseudo symmetry/wrong space group identification. It could be misindexing in some weird way. It could be a second crystal that unfortunately for you had a series of overlaps -especially on high intensity reflections. Good luck, -ed On Jul 19, 2010, at 3:41 AM, 孙庆祥 wrote: Dear Collins and all, Thanks for the reply. Please find the following pdb header. For your information, this is after refmac5 with twin-refinement option selected. This is the best R values that I'm getting. Cutting resolution does not help much in getting the Rs down... HEADERSWISS-MODEL SERVER (pa-JAN-g) COMPNDSS-MODEL REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.96 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 91.56 REMARK 3 NUMBER OF REFLECTIONS : 27851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.42077 REMARK 3 R VALUE(WORKING SET) : 0.42170 REMARK 3 FREE R VALUE : 0.40609 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.4 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH :1.522 REMARK 3 BIN RESOLUTION RANGE LOW:1.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :82.44 REMARK 3 BIN R VALUE (WORKING SET) :0.529 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE:0.622 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.096 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3B11 (A**2) : 8.45 REMARK 3B22 (A**2) : -12.86 REMARK 3B33 (A**2) : 4.41 REMARK 3B12 (A**2) : 0.51 REMARK 3B13 (A**2) :-1.32 REMARK 3B23 (A**2) :-8.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE(A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.812 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUESCOUNTRMSWEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS(A): 1016 ; 0.008 ; 0.022 REMARK 3 BOND ANGLES REFINED
Re: [ccp4bb] A strange case of MR
Your beta and gamma angle in P1 are awfully close to 90 degrees. Are you sure about P1 ? Could it be C2 with beta of 104 ˚ ? I'm assuming the CRYST card below belongs to your structure right ? 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/ On Jul 19, 2010, at 10:54 PM, 孙庆祥 wrote: Hi, Collins, Thanks for the valuable comments. I tried refineing using 2.0A cutoff, but the problem persists. (No Molrep solution is found with R less than 0.7, ). Could you please show me how can I indentify and eliminate the catastrophic error that I'm having with the data? Regards, At 2010-07-19 19:48:35，Collins, Edward J edward_coll...@med.unc.edu wrote: Right. So, you have a good map (not perfect since your CC in fo-fc map is in 80% range- should be in 90%s, but lousy overall statistics. What do the R factors/Rfree look like as a function of resolution? Later in this output file, there are those statistics after each cycle. I just want to know if you have a good R factor and Rfree at low resolution but really bad at high resolution? It is possible, based on the postrefine statistics that you chose to use all of your data, but there was really only good data to about 2.0 angstroms. Depending on how bad the statistics are at high resolution, you could get this bad of an Rfree, but that would be strange. At least, I have never seen the Rfactor at 40% in such a case. high 30% would be more likely. The one bin showed in this file is for the highest resolution (50%) which is pretty bad. If you make your resolution cutoff 20-2.0 angstroms and run for a few cycles, you would see if this is a function of resolution. If those statistics look similar (that is, the low resolution R factor and Rfree are bad too), you have a catastrophic error in your data somewhere. It could be pseudo symmetry/wrong space group identification. It could be misindexing in some weird way. It could be a second crystal that unfortunately for you had a series of overlaps -especially on high intensity reflections. Good luck, -ed On Jul 19, 2010, at 3:41 AM, 孙庆祥 wrote: Dear Collins and all, Thanks for the reply. Please find the following pdb header. For your information, this is after refmac5 with twin-refinement option selected. This is the best R values that I'm getting. Cutting resolution does not help much in getting the Rs down... HEADERSWISS-MODEL SERVER (pa-JAN-g) COMPNDSS-MODEL REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.96 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 91.56 REMARK 3 NUMBER OF REFLECTIONS : 27851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.42077 REMARK 3 R VALUE(WORKING SET) : 0.42170 REMARK 3 FREE R VALUE : 0.40609 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.4 REMARK 3 FREE R VALUE TEST SET COUNT : 1584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH :1.522 REMARK 3 BIN RESOLUTION RANGE LOW:1.561 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :82.44 REMARK 3 BIN R VALUE (WORKING SET) :0.529 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE:0.622 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 984 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.096 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3B11 (A**2) : 8.45 REMARK 3B22 (A**2) : -12.86 REMARK 3B33 (A**2) : 4.41 REMARK 3B12 (A**2) : 0.51 REMARK 3B13 (A**2) :-1.32 REMARK 3B23 (A**2) :-8.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK
