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Newsletter No. 386
November 5, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

OCTOBER 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Thapar R. Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs.
Molecules
. 2018 Oct 27;23(11). pii: E2789. doi: 10.3390/molecules23112789.
Review. PubMed PMID: 30373256.

2: Wagh K, Kreider EF, Li Y, Barbian HJ, Learn GH, Giorgi E, Hraber PT, Decker
TG, Smith AG, Gondim MV, Gillis L, Wandzilak J, Chuang GY, Rawi R, Cai F,
Pellegrino P, Williams I, Overbaugh J, Gao F, Kwong PD, Haynes BF, Shaw GM,
Borrow P, Seaman MS, Hahn BH, Korber B. Completeness of HIV-1 Envelope Glycan
Shield at Transmission Determines Neutralization Breadth
. Cell Rep. 2018 Oct
23;25(4):893-908.e7. doi: 10.1016/j.celrep.2018.09.087. PubMed PMID: 30355496.

3: Novikova M, Adams LJ, Fontana J, Gres AT, Balasubramaniam M, Winkler DC,
Kudchodkar SB, Soheilian F, Sarafianos SG,
Steven AC, Freed EO. Identification of
a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and
Maturation
. MBio. 2018 Oct 16;9(5). pii: e01567-18. doi: 10.1128/mBio.01567-18.
PubMed PMID: 30327442; PubMed Central PMCID: PMC6191540.

4: Calabrese DR, Chen X, Leon EC, Gaikwad SM, Phyo Z, Hewitt WM, Alden S,
Hilimire TA, He F, Michalowski AM, Simmons JK, Saunders LB, Zhang S, Connors D,
Walters KJ, Mock BA, Schneekloth JS Jr. Chemical and structural studies provide a
mechanistic basis for recognition of the MYC G-quadruplex
. Nat Commun. 2018 Oct
12;9(1):4229. doi: 10.1038/s41467-018-06315-w. PubMed PMID: 30315240; PubMed
Central PMCID: PMC6185959.

5: Çağlayan M, Wilson SH. Pol μ dGTP mismatch insertion opposite T coupled with
ligation reveals promutagenic DNA repair intermediate
. Nat Commun. 2018 Oct
11;9(1):4213. doi: 10.1038/s41467-018-06700-5. PubMed PMID: 30310068; PubMed
Central PMCID: PMC6181931.

6: Johnson EL, Doria-Rose NA, Gorman J, Bhiman JN, Schramm CA, Vu AQ, Law WH,
Zhang B, Bekker V, Abdool Karim SS, Ippolito GC, Morris L, Moore PL,
Kwong PD,
Mascola JR, Georgiou G. Sequencing HIV-neutralizing antibody exons and introns
reveals detailed aspects of lineage maturation
. Nat Commun. 2018 Oct 8;9(1):4136.
doi: 10.1038/s41467-018-06424-6. PubMed PMID: 30297708; PubMed Central PMCID:
PMC6175870.

7: Rawi R, Shen CH,
Kwong PDD, Chuang GY. CRISPro: An Automated Pipeline for
Protein Conformation Stabilization by Proline
. J Chem Inf Model. 2018 Oct 19.
doi: 10.1021/acs.jcim.8b00592. [Epub ahead of print] PubMed PMID: 30290119.

8:
Lountos GT, Raran-Kurussi S, Zhao BM, Dyas BK, Burke TR Jr, Ulrich RG, Waugh
DS
. High-resolution crystal structures of the D1 and D2 domains of protein
tyrosine phosphatase epsilon for structure-based drug design
. Acta Crystallogr D
Struct Biol. 2018 Oct 1;74(Pt 10):1015-1026. doi: 10.1107/S2059798318011919. Epub
2018 Oct 2. PubMed PMID: 30289412; PubMed Central PMCID: PMC6173050.

9: Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W. Bypassing a
8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase η at atomic
resolution
. Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):10660-10665. doi:
10.1073/pnas.1812856115. Epub 2018 Oct 1. PubMed PMID: 30275308; PubMed Central
PMCID: PMC6196489.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS FSEARCH: cryo-EM Map Replacement

FSEARCH: cryo-EM Map Replacement |  Recently, a  hybrid method that integrates X-ray crystallography with cryo-EM for structure determination is presented by Lingxiao Zeng, Wei Ding, and Quan Hao in the IUCrJ (5:382-389, 2018). The starting point is a cryo-EM map  and the end point is a high-resolution crystal structure. The workflow of the method and four case study examples can be seen here.

A new MR-SAD algorithm | 
Recently, a  new MR-SAD algorithm was  reported  by Pavol Skubak, Navray Pannu, and co-workers in the IUCrJ (5:166-171, 2018), for automatic building of protein models from low-resolution X-ray diffraction data and a poor starting model. According to the authors, their algorithm uses a multivariate function to simultatnerously exploit informatino from both the initial partial model and low-resolution SAD data. Details of the algorithm and its application to six challenging structure determinations can be seen here.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Biophysical Methods.

TOPIC DISCUSSIONTable 1

A perspective article "Against Method: Table 1--Cui Bono?" was  recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scrutiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from preferably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."

Do you agree with Bernhard? Please share your opinion and ideas with fellow crystallographers.

Dr. Mariusz Jackolski: "Dr. Xinhua Ji has encouraged discussion on the somewhat controversial proposition of Dr. Bernhard Rupp to get rid of Table 1 from published crystallographic papers.  As much as I sympathize with Bernhard's crusade to wed "post modern relativism" from exact science, I am not sure that his aim at Table 1 is well advised.  I am afraid that his proposition could have the opposite effect, i.e., could accelerate the demise of something that is perhaps not perfect but certainly very useful; in the end Table 1 would be replaced by just nothing.  Bernhard is giving strong arguments to the opponents of any kind of Table 1 information in experimental papers.  If we want to maintain high standard in crystallographic literature, we should work out a concrete (improved) alternative to Table 1 and start using it in practice."

 

Dr. Peter D. Sun: “I do not agree with the author of the perspective article in Structure.  I think one has to ask who reads Table 1 and how useful it is in a crystallographic structure publication.  Without giving too much thought, I think  Table 1 is very useful to most non-crystallographic trained but structurally tuned readers—which probably makes up the majority of the scientists who are interested in crystal structures.  Majority of them do care about resolution and a few also care about R-factors.  Table 1 serves primarily the purpose of announcing the birth of a “new” structure with certain attributes to allow general public to assess the quality and compare the current on with any other structures they know of.   In the past, crystallographic community have relied on Table 1 to evaluate a structure for its correctness.  It is true that the information in the table is insufficient to repeat the experiment and in many cases indifferent to minor errors in structures.  However, in this day and age and with the exception of few, most of crystallographers read structural publications for new scientific insights and structural information, not with a purpose to validate and repeat the published structures.  This is mostly due to the software development in our field. 

Secondly, I would caution to use highly specialized statistics for data quality representation.  Even though such representation, such as unmerged intensity data with graphical presentation of reciprocal space features, may indeed reflect more accurately the state of a refined model, they are less comprehensive to our audience, and thus less useful.  In fact, it is not clear how many crystallographers understand the errors and their propagation in our models. 

In anycase, my point is a structural publication is best regarded as an illustration to a new consumer product.  It is for the interest of general audience.  For a few specialized experts, then again, there is PDB. 

I do however, think it benefits the community to shorten the Table 1, so that the critical information can be easily discerned in main text not through supplemental as most of Table 1’s are.”

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation.

LECTURES AND TUTORIALS CRYSTALLOGRAPHY


DR. ZBIGNIEW DAUTER'S LECTURES AT THE NIH (2005)
 

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

            with possible use of it for phasing"


RIGAKU WEBINAR SERIES (2009 - PRESENT)

LOW RESOLUTION PHASING AND REFINEMENT (2011)

CRYSTALLOGRAPHY: SEEING THINGS IN A DIFFERENT LIGHT (2013)

CRYSTALLOGRAPHY: FOR ASPIRING CRYSTALLOGRAPHERS (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

A GLIMPSE OF STRUCTURAL BIOLOGY THROUGH X-RAY CRYSTALLOGRAPHY (2014)

CRYSTAL CLEAR (2014)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 LINKS - Suggestions?

Databases: BMCDDisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, Phyre, MolProbity, Protein, Robetta Fragment, HHpred,
 
            RestraintLib,


Facilities: 
APS SER-CAT, APS SAXS Capabilities

 
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (http://mcl1.ncifcrf.gov)