Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
It was published in Nature so it must be right :) ... Dear crystallographers, The PDB entry http://www.rcsb.org/pdb/explore.do?structureId=3BDNhttp://www.rcsb.org/pdb/explore.do?structureId=3BDN has 16.5% Ramachandran outliers. When I opened this PDB file in coot and checked for Ramachandran outliers, the results are: In preffered region: 58.04% In allowed regions: 19.78% Outliers: 22.17% ! With an R-free of 37.4% at 3.9 A resolution, could you please tell me how reliable this structure of Lambda repressor bound to DNA is? Thanks Misbha -- +++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://snb.nichd.nih.gov/index.htm Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892
Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
Its not just the Ramachandran outliers - the attached metrics summary courtesy of the PDB raises a lot of questions about the accuracy of this structure As for Nature being right, it was an attempt at humor. Dear crystallographers, The PDB entry http://www.rcsb.org/pdb/explore.do?structureId=3BDNhttp://www.rcsb.org/pdb/explore.do?structureId=3BDN has 16.5% Ramachandran outliers. When I opened this PDB file in coot and checked for Ramachandran outliers, the results are: In preffered region: 58.04% In allowed regions: 19.78% Outliers: 22.17% ! With an R-free of 37.4% at 3.9 A resolution, could you please tell me how reliable this structure of Lambda repressor bound to DNA is? Thanks Misbha -- +++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://snb.nichd.nih.gov/index.htm Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 3BDN_metrics.png Description: Binary data
[ccp4bb] DSSP and PDB secondary structure assignments
I've recently noticed that the Helix and Sheet records in PDB entries differ from those generated by DSSP and would like to ask if anyone can explain how the PDB makes the assignments. Until now I'd always assumed that the PDB and DSSP records were the same. As an example I've listed a few lines from 2V3U.pdb. There are similar difference in both helix lengths and start/stop positions that occur in 9 other entries I've looked at. 2V3U.pdb HELIX1 1 GLY A 31 GLY A 45 1 15 HELIX2 2 ASN A 68 PHE A 76 1 9 HELIX3 3 THR A 89 ASN A 94 1 6 and for the same structure the DSSP entry from the CMBI data base http://swift.cmbi.ru.nl/gv/dssp/ REMARK 1 secondary structure assigned by dssp HELIX1 1 PHE A 32 LEU A 44 1 13 HELIX2 2 GLY A 69 VAL A 75 1 7 HELIX3 3 PRO A 90 GLU A 93 1 4 Its not a big deal, but makes comparing secondary structures a bit more difficult. -- Mark
[ccp4bb] Postdoctoral Fellowship in Membrane Protein Structural Biology at NIH
Structural studies on glutamate receptor ion channels: A postdoctoral position in X-ray crystallography is available immediately in the group of Dr. Mark L. Mayer, in the Laboratory of Cellular and Molecular Neurophysiology at the NIH in Bethesda MD, USA. This opening is part of an established program with a long term focus on glutamate receptor ion channels: see http://snb.nichd.nih.gov/index.htm for recent publications and research interests. Substantial efforts have already been undertaken in construct design, protein expression and detergent screening, leading to very promising leads for crystallization. The laboratory is located in the main NIH campus. We have shared state-of-the-art facilities large scale eukaryotic cell culture, and for crystallization, in-house X-ray data collection and other biophysical approaches. We also have regular synchrotron beamtime at the Advanced Photon Source (APS) through membership of SER-CAT. Interested applicants must have a Ph.D. in biochemistry, molecular biology or structural biology, extensive experience in protein expression and purification, and X-ray crystallography. Experience working with insect cell culture and baculovirus expression systems would be an advantage is but not essential. The ideal candidate will be highly motivated, possess excellent communication skills and the ability to work in a collaborative and team-oriented environment. To apply, please e-mail a CV including a list of publications, a brief statement of experience and scientific interests, and contact information for three references to may...@mail.nih.gov Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 --
[ccp4bb] UV microscopes for Xtal visualization
I have read the paper by Gill in Acta Crys F66: 364-372 and wonder what other peoples experience has been with the MUVIS from Formulatrix and the JANsci microscope for imaging 96 well plates. The JANsci instrument seems to have an advantage over the MUVIS in having two objectives. For detecting small xtals in LCP will the low field objective of the MUVIS be useful? Thanks, Mark --
Re: [ccp4bb] Deposition of riding H: R-factor is overrated
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the
the riding H discussion, my mtz file had Fc Phic FOM + other data put
out by Phenix - pavel can elaborate. rcsb stripped almost all of this
and the processed file has only:
HKL, Flag, Fc, SigmaF and FOC :{
What's a structural biologist to do?
--
Mark
[ccp4bb] Deposition of riding H: R-factor is overrated
Huh? That's not a cif fragment. What file are you looking at? In my experience the PDB feeds back to you a cif format structure factor file with a name like rcsb054058-sf.cif Near the top of that file you should find a description of the data columns. The columns present depend on what you fed it, of course. Come on guys - give me a break ... all I posted was just a list of the columns in the sf file - here's a cut and paste of what rcsb actually generated rcsb061284-sf.cif data_r3om0sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record'Initial release' loop_ _refln.wavelength_id _refln.crystal_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.F_meas_au _refln.F_meas_sigma_au _refln.fom 1 1 1 008 o 203.06.3 0.99 1 1 1 00 10 o 281.58.7 0.86 Below is mtzdmp of what I actually deposited (as MTZ) Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 46 0 100.00 17.7 17.7 31.88 1.40 H H 2 NONE 0 72 0 100.00 27.4 27.4 31.88 1.40 H K 3 NONE 0 81 0 100.00 30.5 30.5 31.88 1.40 H L 4 NONE3.3 2160.3 0 100.00 162.89 162.89 31.88 1.40 F FOBS 5 NONE0.960.0 0 100.00 5.36 5.36 31.88 1.40 Q SIGFOBS 6 NONE0.0 1.0 0 100.00 0.05 0.05 31.88 1.40 I R_FREE_FLAGS 7 NONE0.1 2253.6 0 100.00 157.73 157.73 31.88 1.40 F FMODEL 8 NONE -180.0 180.0 0 100.00 2.6590.13 31.88 1.40 P PHIFMODEL 9 NONE0.0 5823.1 0 100.00 219.29 219.29 31.88 1.40 F FCALC 10 NONE -180.0 180.0 0 100.00 3.2490.09 31.88 1.40 P PHIFCALC 11 NONE0.0 15330.0 0 100.00 141.04 141.04 31.88 1.40 F FMASK 12 NONE -180.0 180.0 0 100.00 4.2990.74 31.88 1.40 P PHIFMASK 13 NONE0.0 6909.4 0 100.0015.4215.42 31.88 1.40 F FBULK 14 NONE -180.0 180.0 0 100.00 4.2990.74 31.88 1.40 P PHIFBULK 15 NONE 0.803 1.199 0 100.001.0041.004 31.88 1.40 W FB_CART 16 NONE 0.001 1.000 0 100.000.8770.877 31.88 1.40 W FOM 17 NONE 0.576 0.754 0 100.000.7050.705 31.88 1.40 W ALPHA 18 NONE277.388 0 100.00 5655.391 5655.391 31.88 1.40 W BETA -- Mark
Re: [ccp4bb] Deposition of riding H
However this thread appears to have reached the point where not much new ground is being broken. As the person who started this thread I'll second Phil Jeffrey's comment. I chose to continue my depositions with riding H, and the rcsb agreed to accept the coordinates. Its been great hearing the experts weigh in on this. I've learned a lot, and clearly there is no consensus. As one of the vast majority of crystallographers dependent on all the hard work that program developers undertake to support structural biology, I'm happy to follow advice given by the developers of the various programs I use, and for Phenix the current advice is to deposit with riding H. -- Mark
[ccp4bb] Deposition of riding H
Here's one for the community, which I'll post to both Phenix and CCP4 BBs. Where does the crystallographic community stand on deposition of coordinates with riding hydrogens? Explicit H are required for calculating all atom clash scores with Molprobity, and their use frequently gives better geometry (especially at low resolution). Phenix uses explicit riding H for refinement, and outputs these in the refined PDB. Refmac also uses riding H but does not output H coordinates. While depositing a series of structures refined at 1.4 - 2.75 A with Phenix got the following email from the RCSB, who asked I resupply coordinates without H for two of the structures. Since we can't see H even at 1.4 Å I don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why explicit H atoms used in refinement and geometry validation should be stripped from the file. FROM RCSB We encourage depositors not to use hydrogens in the final PDB file for the low resolution structures ( 1.5 A). Please provide an updated PDB file. We request you to use processed PDB file as a starting point for making any corrections to the coordinates and/or re-refinement. -- Mark
[ccp4bb] how to improve Rfree?
You can also pick thin shells with SFCHECK and with 12-fold NCS the referees will likely not be kind if you dont!!! -- Mark
[ccp4bb] Slightly off-topic - silica based columns
Slightly off-topic - but these days most crystallographers are interested in protein purification. What experience do people have with silica based columns for size exclusion chromatography. We are interested in resolution, stability, column life time, and ease of cleaning column compared to Superdex and Superose columns. Please describe specific columns if you can. Thanks -- Mark Mayer
