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Newsletter No. 328
February 1, 2016

ACA News, IUCr Newsletter, IUCr Meetings List

JANUARY 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Tang WK, Xia D. Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and
ATPase Activity of the D1-domain
. Sci Rep. 2016 Jan 28;6:20037. doi:
10.1038/srep20037. PubMed PMID: 26818443.

2: Biter AB, de la Peña AH, Thapar R, Lin JZ, Phillips KJ. DSF Guided Refolding
As A Novel Method Of Protein Production
. Sci Rep. 2016 Jan 19;6:18906. doi:
10.1038/srep18906. PubMed PMID: 26783150; PubMed Central PMCID: PMC4726114.

3: Zhang J,
Ferré-D'Amaré AR. The tRNA Elbow in Structure, Recognition and
Evolution
. Life (Basel). 2016 Jan 12;6(1). pii: E3. doi: 10.3390/life6010003.
Review. PubMed PMID: 26771646.

4: Bakelar J, Buchanan SK, Noinaj N. The structure of the β-barrel assembly
machinery complex
. Science. 2016 Jan 8;351(6269):180-6. doi:
10.1126/science.aad3460. PubMed PMID: 26744406.

5: Venditti V, Egner TK, Clore GM. Hybrid Approaches to Structural
Characterization of Conformational Ensembles of Complex Macromolecular Systems
Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering
. Chem Rev.
2016 Jan 7. [Epub ahead of print] PubMed PMID: 26739383.

6:
Dauter Z, Wlodawer A. Progress in protein crystallography. Protein Pept Lett.
2016 Jan 6. [Epub ahead of print] PubMed PMID: 26732246.

7: Shindo S, Moore R, Negishi M. Detection and Functional Analysis of Estrogen
Receptor α Phosphorylated at Serine 216 in Mouse Neutrophils
. Methods Mol Biol.
2016;1366:413-24. doi: 10.1007/978-1-4939-3127-9_32. PubMed PMID: 26585153.

8:
Ferré-D'Amaré AR. Use of the U1A Protein to Facilitate Crystallization and
Structure Determination of Large RNAs
. Methods Mol Biol. 2016;1320:67-76. doi:
10.1007/978-1-4939-2763-0_6. PubMed PMID: 26227038.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS cryoEM and SAXS

Cryo-electron microscopy (cryoEM) is an ensemble of techniques allowing the observation of biological specimens in their native environment at cryogenic temperatures in EM. For a recent cryoEM structure at high resolution, please see 2.2 Å resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor. For an overview, please see CryoEM at IUCrJ: a new era.

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 DISCUSSIONCrystal Structures

Mariusz Jaskolski: Geometrical Restraints of His Residues

A recent paper, already listed on this bulletin board, will give you a hint about improving the geometrical restraints of His residues, depending on their protonation/tautomeric form, especially at high resolution:

M.Malinska, M.Dauter, M.Kowiel, M.Jaskolski, Z.Dauter (2015) Protonation and geometry of histidine rings. Acta Cryst. D71, 1444-1454.

This may be a good occasion to mention that for years Refmac has been using the older (1991) version (containing errors) of the Engh & Huber stereochemical dictionary, even though the authors themselves (E&H) corrected it in 2001...

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)