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Newsletter No. 325
December 7, 2015

ACA News, IUCr Newsletter, IUCr Meetings List

NOVEMBER 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Libich DS, Tugarinov V, Clore GM. Reply to Marchenko et al.: Flux analysis of 
GroEL-assisted protein folding/unfolding
. Proc Natl Acad Sci U S A. 2015 Nov 24.
pii: 201520474. [Epub ahead of print] PubMed PMID: 26604310.

2: Çağlayan M, Wilson SH. Reprint of "Oxidant and environmental toxicant-induced
effects compromise DNA ligation during base excision DNA repair"
. DNA Repair
(Amst). 2015 Nov 12. pii: S1568-7864(15)00217-7. doi:
10.1016/j.dnarep.2015.11.002. PubMed PMID: 26596511.

3: Shcherbakova DM, Baloban M, Pletnev S, Malashkevich VN, Xiao H, Dauter Z,
Verkhusha VV. Molecular Basis of Spectral Diversity in Near-Infrared
Phytochrome-Based Fluorescent Proteins
. Chem Biol. 2015 Nov 19;22(11):1540-51.
doi: 10.1016/j.chembiol.2015.10.007. PubMed PMID: 26590639.

4: Yang W, Lee YS. A DNA-hairpin model for repeat-addition processivity in
telomere synthesis
. Nat Struct Mol Biol. 2015 Nov 4;22(11):844-7. doi:
10.1038/nsmb.3098. PubMed PMID: 26581517.

5: Hickman AB, Dyda F. The casposon-encoded Cas1 protein from Aciduliprofundum
boonei is a DNA integrase that generates target site duplications
. Nucleic Acids
Res. 2015 Nov 16. pii: gkv1180. [Epub ahead of print] PubMed PMID: 26573596.

6: Xia D, Ye Y. In Search of a Cure for Proteostasis-Addicted Cancer: A AAA
Target Revealed
. Cancer Cell. 2015 Nov 9;28(5):550-2. doi:
10.1016/j.ccell.2015.10.006. PubMed PMID: 26555170.

7: Xu P, Xu M, Jiang L, Yang Q, Luo Z, Dauter Z, Huang M, Andreasen PA. Design of
Specific Serine Protease Inhibitors Based on a Versatile Peptide Scaffold:
Conversion of a Urokinase Inhibitor to a Plasma Kallikrein Inhibitor
. J Med Chem.
2015 Nov 25;58(22):8868-76. PubMed PMID: 26536069.

8: Dauter Z,
Wlodawer A. On the accuracy of unit-cell parameters in protein
crystallography
. Acta Crystallogr D Biol Crystallogr. 2015 Nov 1;71(Pt
11):2217-26. doi: 10.1107/S1399004715015503. PubMed PMID: 26527139.

9:
Wlodawer A. Editorial - Introducing Structural Snapshots. FEBS J. 2015 Nov 2.
doi: 10.1111/febs.13583. [Epub ahead of print] PubMed PMID: 26524689.

10: Louis JM, Baber JL, Clore GM. The C34 Peptide Fusion Inhibitor Binds to the
Six-Helix Bundle Core Domain of HIV-1 gp41 by Displacement of the C-Terminal
Helical Repeat Region
. Biochemistry. 2015 Nov 17;54(45):6796-805. doi:
10.1021/acs.biochem.5b01021. Epub 2015 Nov 9. PubMed PMID: 26506247.

11: Lu J, Sun PD. Structural mechanism of high affinity FcγRI recognition of
immunoglobulin G
. Immunol Rev. 2015 Nov;268(1):192-200. doi: 10.1111/imr.12346.
Review. PubMed PMID: 26497521.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - SAXS (small-angle X-ray scattering)

Small-angle X-ray scattering (SAXS) is capable of delivering structural information of biological macromolecules and their complexes in solution, small or large. For a recent example, the SAXS model for a ~500-kDa RapA:RNA polymerase complex (~230 angstroms in its longest dimension), please see Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies.

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

TOPIC DISCUSSION - Suggestions?

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

LECTURES AND TUTORIALS - Dr. Dauter's Lectures Are Back!

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)

NATIVE SAD IS MATURING (2015)

 LINKS - Suggestions?     

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry Database, Scattering

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


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, PhyreProbity, Protein, Robetta Fragment & HHpred  

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)