| Newsletter No. 375
|| April 16, 2018
ACA 2018, FEBS 2018, Protein Society 2018
1: Grabundzija I, Hickman AB, Dyda F. Helraiser intermediates provide insight
| 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.
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 Crystallography, Absorption Correction, Data for Refinement and Publication, Validation.
| 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: BMCD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDB, PDB, PDBe,
Protein Geometry, Scattering
Programs: CCP4, COOT, DSSR, HKL, PHENIX, PyMOL, SOLVE, XDS
Servers: ACHESYM, Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript,
Grade, PDBePISA, Phyre, MolProbity, 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)|