e16.html

1. The NIH meeting "Structural Analysis of Large Macromolecular Assemblies: Sizing Up the Challenges" <http://pub.nigms.nih.gov/generic_meeting/index.cfm?id=7> June 2-3.

1: Prasanna MD, Vondrasek J, Wlodawer A, Bhat TN.
Application of InChI to curate, index, and query 3-D structures.
Proteins. 2005 Apr 28; PMID: 15861385

2: Cohen GH, Silverton EW, Padlan EA, Dyda F, Wibbenmeyer JA, Willson RC, Davies DR.
Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.
Acta Crystallogr D. 2005 May;61(Pt 5):628-33. PMID: 15858274

3: Miller GJ, Wilson MP, Majerus PW, Hurley JH.
Specificity determinants in inositol polyphosphate synthesis: crystal structure of inositol 1,3,4-trisphosphate 5/6-kinase.
Mol Cell. 2005 Apr 15;18(2):201-12. PMID: 15837423

4: Gustchina E, Hummer G, Bewley CA, Clore GM.
Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV.
J Med Chem. 2005 Apr 21;48(8):3036-44. PMID: 15828842

5: Garboczi DN.
Structural biology. "D" is not for diversity.
Science. 2005 Apr 8;308(5719):209-10. PMID: 15821077

6: Gustchina A, Li M, Wunschmann S, Chapman MD, Pomes A, Wlodawer A.
Crystal structure of cockroach allergen Bla g 2, an unusual zinc binding
aspartic protease with a novel mode of self-inhibition.
J Mol Biol. 2005 Apr 29;348(2):433-44. PMID: 15811379

7: Snyder GA, Ford J, Torabi-Parizi P, Arthos JA, Schuck P, Colonna M, Sun PD.
Characterization of DC-SIGN/R interaction with human immunodeficiency virus type 1 gp120 and ICAM molecules favors the receptor's role as an antigen-capturing rather than an adhesion receptor.
J Virol. 2005 Apr;79(8):4589-98. PMID: 15795245

8: Snyder GA, Colonna M, Sun PD.
The structure of DC-SIGNR with a portion of its repeat domain lends insights to modeling of the receptor tetramer.
J Mol Biol. 2005 Apr 15;347(5):979-89. PMID: 15784257

9: Guan R, Wang Q, Sundberg EJ, Mariuzza RA.
Crystal structure of human peptidoglycan recognition protein S (PGRP-S) at 1.70 A resolution.
J Mol Biol. 2005 Apr 8;347(4):683-91. PMID: 15769462

10: Hansen AM, Gu Y, Li M, Andrykovitch M, Waugh DS, Jin DJ, Ji X.
Structural basis for the function of stringent starvation protein a as a
transcription factor.
J Biol Chem. 2005 Apr 29;280(17):17380-91. PMID: 15735307

11: Shi D, Morizono H, Yu X, Roth L, Caldovic L, Allewell NM, Malamy MH, Tuchman M.
Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria.
J Biol Chem. 2005 Apr 15;280(15):14366-9. PMID: 15731101

12: Park H, Adsit FG, Boyington JC.
The 1.4 anstrom crystal structure of the human oxidized low density lipoprotein receptor lox-1.
J Biol Chem. 2005 Apr 8;280(14):13593-9. PMID: 15695803

HKL2000 has a built-in feature (Reprocess) to reintegrate raw date (frames) with unit cell parameters fixed at the values obtained after postrefinement using Scalepack. Any comments, experience, or recommendations?

Lothar Esser (NCI): I just read Dr. Garboczi's Topic Discussion on HKL2000 vs XDS. As you said there may be something I can add in particular with regard to absorption correction. But let's go through the items in order.

My take on refining cell dimensions in Denzo is this that Denzo's job is to locate each spot and integrate the intensity that belongs to a particular Miller index. This is done by predicting the location of each spot based on crystal orientation, a variety of geometric factors of the experimental setup and of course on the current cell dimensions. If we were to say that cell dimensions are not to be refined (other than the necessarily fixed ones in a given crystal system) 'because a crystal can have only one fixed set of cell dimensions', we are shifting the burden of keeping a good match between observations and predictions to all other refinable parameters. Can this be done ? In an ideal world the answer is "yes", in reality the answer is "perhaps in some cases". So are cell dimensions changing or is the refinement of them only a means of inflating the number of parameters (over fitting?)

1) Crystal decay. There is no reason to believe that a crystal that decays will doggedly cling to its initial cell dimensions. Effects like local dehydration, decarboxylation, bond cleavage and more come to mind that could alter the cell.

Again what I want from Denzo is the best possible estimate of the intensity/background that belongs to a particular Miller index. If this requires refinement of cell dimensions I have no objections. The final question is can Denzo do it ? It is the task then of the crystallographer to analyze the behavior of any drifts in the cell and intervene with fixing some parameters (like distance, crossfire etc) or even "Special Integration" if necessary.

Besides problems with twins and satellites, I can think of only one reason why you might need to fix the cell dimensions, and that is when a crystal is unusually accurately aligned and the diffraction pattern provides not enough variation in one dimension.

That said, in my experience, denzo_3d does a very good job overall even when mostly default options are being used including the refinement of cell dimensions.

(Quite frankly I worry more about what the correct spot radius/ ellipse might be if my spots are smeared or elongated in different directions in different parts of the image.)

The default license won't include Absorption Correction (zo3). Request a new license with this feature included.

David Garboczi (NIAID): I used to do this with the script form of denzo. I've read and thought that refining the cell during integration was a little suspect. After all, if one can't trust that the cell dimensions are fixed enough to define your crystal, maybe that crystal isn't worth it. Mosflm finds the cell dimensions first and then integrates. I would definitely recommend reprocessing and would like to know about the other buttons in HKL2000 For instance, our absorption correction button clicks like it works, but the logfile says "Unknown keyword: absorption".

We are using XDS a lot as well and like its complete and current documentation. Its radiation damage correction algorithm has helped our anomalous signal, such that I doubt we would have solved several structures without it.