logo2a.gif

Newsletter No. 329
February 15, 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: Pathological Behavior of Atomic Occupancy Factors
A number of PDB files have been detected and reported by Zbyszek Dauter, in which the atomic occupancy factors show a pathological behavior, where covalently connected atoms have uncorrelated fractional occupancies.  This pathology seems to have been spreading unnoticed because MR-generated structures inherited the pathology from some earlier models, and the refinement programs were not rigorous enough to block (or at least signal) the "infection".  You might be advised to check your PDB files for this pathology, using an ad-hoc server http://achesym.ibch.poznan.pl/occucheck/ by Marcin Kowiel.

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)