| Newsletter No. 380
|| July 2, 2018
ACA 2018, FEBS 2018, Protein Society 2018
1: Mishra V, Rathore I, Arekar A, Sthanam LK, Xiao H, Kiso Y, Sen S, Patankar S,
| 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 - Table 1
A perspective article "Against Method: Table 1--Cui Bono?" was recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scruitiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from prefereably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."
Do you agree with Bernhard? Please share your opionion and ideas with fellow crystallographers.
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)|