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Newsletter No. 346
December 19, 2016

NIH's First Structures by XFEL Crystallography

ACA News, IUCr Newsletter, IUCr Meetings List

NOVEMBER 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ,
Zhou T,
Kwong PD, Shapiro L, Honig B, Friesner RA. Free Energy Perturbation
Calculation of Relative Binding Free energy between Broadly Neutralizing
Antibodies and the gp120 Glycoprotein of HIV-1
. J Mol Biol. 2016 Nov 28. pii:
S0022-2836(16)30516-2. doi: 10.1016/j.jmb.2016.11.021. [Epub ahead of print]
PubMed PMID: 27908641.

2: Li Y, Dharkar P, Han TH, Serpe M, Lee CH, Mayer ML. Novel Functional
Properties of Drosophila CNS Glutamate Receptors
. Neuron. 2016 Nov 21. pii:
S0896-6273(16)30808-X. doi: 10.1016/j.neuron.2016.10.058. [Epub ahead of print]
PubMed PMID: 27889096.

3: Lau MW,
Ferré-D'Amaré AR. Many Activities, One Structure: Functional
Plasticity of Ribozyme Folds
. Molecules. 2016 Nov 18;21(11). pii: E1570. Review.
PubMed PMID: 27869745.

4: Bakelar J, Buchanan SK, Noinaj N. Structural snapshots of the β-barrel
assembly machinery
. FEBS J. 2016 Nov 14. doi: 10.1111/febs.13960. [Epub ahead of
print] Review. PubMed PMID: 27862971.

5: Schmidt T, Wälti MA, Baber JL, Hustedt EJ,
Clore GM. Long Distance
Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR
Spectroscopy
. Angew Chem Int Ed Engl. 2016 Nov 17. doi: 10.1002/anie.201609617.
[Epub ahead of print] PubMed PMID: 27860003.

6: Huang J, Kang BH, Ishida E, Zhou T, Griesman T, Sheng Z, Wu F, Doria-Rose NA,
Zhang B, McKee K, O'Dell S, Chuang GY, Druz A, Georgiev IS, Schramm CA, Zheng A,
Joyce MG, Asokan M, Ransier A, Darko S, Migueles SA, Bailer RT, Louder MK, Alam
SM, Parks R, Kelsoe G, Von Holle T, Haynes BF, Douek DC, Hirsch V, Seaman MS,
Shapiro L, Mascola JR,
Kwong PD, Connors M. Identification of a CD4-Binding-Site
Antibody to HIV that Evolved Near-Pan Neutralization Breadth
. Immunity. 2016 Nov
15;45(5):1108-1121. doi: 10.1016/j.immuni.2016.10.027. PubMed PMID: 27851912.

7: Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G,
Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA,
Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J,
Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo
X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX.
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial
crystallography
. Nature. 2016 Nov 14. doi: 10.1038/nature20599. [Epub ahead of
print] PubMed PMID: 27841871.

8: Strickland M, Stanley AM, Wang G, Botos I, Schwieters CD, Buchanan SK,
Peterkofsky A, Tjandra N. Structure of the NPr:EIN(Ntr) Complex: Mechanism for
Specificity in Paralogous Phosphotransferase Systems
. Structure. 2016 Nov 8. pii:
S0969-2126(16)30315-X. doi: 10.1016/j.str.2016.10.007. [Epub ahead of print]
PubMed PMID: 27839951.

9: Deshmukh L, Louis JM, Ghirlando R,
Clore GM. Transient HIV-1 Gag-protease
interactions revealed by paramagnetic NMR suggest origins of compensatory drug
resistance mutations
. Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12456-12461.
PubMed PMID: 27791180; PubMed Central PMCID: PMC5098610.

10: Yu A, Alberstein R, Thomas A, Zimmet A, Grey R,
Mayer ML, Lau AY. Molecular
lock regulates binding of glycine to a primitive NMDA receptor
. Proc Natl Acad
Sci U S A. 2016 Nov 1;113(44):E6786-E6795. PubMed PMID: 27791085; PubMed Central
PMCID: PMC5098608.

11: Batra VK, Beard WA, Pedersen LC, Wilson SH. Structures of DNA Polymerase
Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an
Induced-Fit Fidelity Mechanism
. Structure. 2016 Nov 1;24(11):1863-1875. doi:
10.1016/j.str.2016.08.006. PubMed PMID: 27642161; PubMed Central PMCID:
PMC5093059.

12: Zhang D,
Wlodawer A, Lubkowski J. Crystal Structure of a Complex of the
Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains
of Human JAK1
. J Mol Biol. 2016 Nov 20;428(23):4651-4668. doi:
10.1016/j.jmb.2016.10.005. PubMed PMID: 27725180.

13: Esser L, Zhou F, Zhou Y, Xiao Y, Tang WK, Yu CA, Qin Z, Xia D. Hydrogen
Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking
to the Quinol Oxidation Site of Complex III
. J Biol Chem. 2016 Nov
25;291(48):25019-25031. PubMed PMID: 27758861; PubMed Central PMCID: PMC5122771.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS Restraint Libraries for Nucleic Acids

Mariusz Jaskolski: Stereochemical Restraint Libraries for Nucleic Acids

As part of a project aimed at revising the stereochemical restraint libraries for nucleic acids, a server, RestraintLib, has been created. It prepares external (custom) restraint files for the phosphate groups in DNA and RNA structures (submitted as PDB files). At present, the output is prepared for Refmac5, but other formats will be added as well.

The discussion of the new restraints and the method of their generation are presented in Nucleic Acids Research Advanced Access published August 12, 2016.


Zbigniew Dauter (NCI): Data Completeness from HKL2000 or HKL3000

Sometimes, relatively weak diffraction data processed with HKL2000 or HKL3000 show lower than expected completeness in the high resolution bins, in spite of otherwise high multiplicity and coverage of the reciprocal space. Apparently, this results from the automatic rejection of weak reflections, for which there are no good enough neighbors for building a “standard profile” within the vicinity defined by default value of the “Profile Fitting Radius”. To increase the high-resolution data completeness one can change the default profile fitting radius (in the “Index” window of HKL2000 or HKL3000) to much larger value, e.g. one third of the detector size. The number of “good” reflections, e.g. stronger than 5s(I), within the profile fitting radius can be visualized at the Xdisp window by clicking the “Prof Fit R” option.

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

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.

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 - New Server: RestraintLib
  

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,
 
            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)