logo3

Newsletter No. 377
May 21, 2018

The Fascinating World of Crystallography

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2018, FEBS 2018, Protein Society 2018

APRIL 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Rutten L, Lai YT, Blokland S, Truan D, Bisschop IJM, Strokappe NM, Koornneef
A, van Manen D, Chuang GY, Farney SK, Schuitemaker H,
Kwong PD, Langedijk JPM. A
Universal Approach to Optimize the Folding and Stability of Prefusion-Closed
HIV-1 Envelope Trimers
. Cell Rep. 2018 Apr 10;23(2):584-595. doi:
10.1016/j.celrep.2018.03.061. PubMed PMID: 29642014.

2: Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S, Guynet C, Hickman AB,
Chandler M,
Dyda F, Barabas O. Targeting IS608 transposon integration to highly
specific sequences by structure-based transposon engineering
. Nucleic Acids Res.
2018 Apr 9. doi: 10.1093/nar/gky235. [Epub ahead of print] PubMed PMID: 29635476.

3:
Dauter Z, Wlodawer A. Unexpected Specificity of a Trypsin-like Enzyme.
Structure. 2018 Apr 3;26(4):530-531. doi: 10.1016/j.str.2018.03.007. PubMed PMID:
29617650.

4: Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M,
Yang W.
Cracking the DNA Code for V(D)J Recombination. Mol Cell. 2018 Apr
19;70(2):358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Epub 2018 Apr 5. PubMed
PMID: 29628308.

5: Shivatare VS, Shivatare SS, Lee CD, Liang CH, Liao KS, Cheng YY, Saidachary G,
Wu CY, Lin NH,
Kwong PD, Burton DR, Wu CY, Wong CH. Unprecedented Role of Hybrid
N-Glycans as Ligands for HIV-1 Broadly Neutralizing Antibodies
. J Am Chem Soc.
2018 Apr 18;140(15):5202-5210. doi: 10.1021/jacs.8b00896. Epub 2018 Apr 9. PubMed
PMID: 29578688.

6: Rawi R, Mall R, Kunji K, Shen CH,
Kwong PD, Chuang GY. PaRSnIP: sequence-based
protein solubility prediction using gradient boosting machine
. Bioinformatics.
2018 Apr 1;34(7):1092-1098. doi: 10.1093/bioinformatics/btx662. PubMed PMID:
29069295.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - 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 DISCUSSION - Protein Structure Prediction

According to Dr. Jason Stagno, the Protein Structure Prediction Center in UC Davis will have another round of CASP starting this coming May and ending in August. Last CASP (CASP12, 2016)  they secured more than 80 targets for prediction and hope that the structural biology community will help them to get as least as many for this CASP (CASP13, 2018). If you already have or will be having non-trivial for prediction structures (sequence identity < 50%), in the closest few months, please consider submitting them to CASP13 following the link here.

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)