| Newsletter No. 392
|| February 18, 2019
ACA 2019, FEBS 2019, Protein Society 2019
1: Lo YH, Sobhany M, Hsu AL, Ford BL, Krahn JM, Borgnia MJ, Stanley RE. Cryo-EM
| TIPS, TRICKS, METHODS - New
Detergent-Free System for Membrane
Protein Structural Biology
Detergent-Free Membrane Protein System | In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure.
FSEARCH: cryo-EM Map Replacement | Recently, a hybrid method that integrates X-ray crystallography with cryo-EM for structure determination is presented by Lingxiao Zeng, Wei Ding, and Quan Hao in the IUCrJ (5:382-389, 2018). The starting point is a cryo-EM map and the end point is a high-resolution crystal structure. The workflow of the method and four case study examples can be seen here.
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 - Suggestions?
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, Table 1.
| 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 (https://mcl1.ncifcrf.gov)|