| Newsletter No. 330
|| March 7, 2016
| TIPS, TRICKS AND METHODS - Widening the Reach of Structural Biology
Micro-electron diffraction (MicroED) data is collected from small 3D microcrystals using a very low electron dose and readily processed using MOSFLM. Using the MicroED approach, the structure of lysozyme was solved using at 2.5-angstrom resolution (PDB entry 3J6K) and the structure of the toxic core of alpha-synuclein was determined at 1.4-angstrom resolution (PDB entry 4RIL). For a review, please see Protein structure determination by MicroED.
Cryo-electron microscopy (CryoEM) is an ensemble of techniques allowing the observation of biological specimens in their native environment at cryogenic temperatures in EM. For a recent cryoEM structure at high resolution, please see 2.2 Å resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor. For an overview, please see CryoEM at IUCrJ: a new era.
Small-angle X-ray scattering (SAXS) is capable of delivering structural information of biological macromolecules and their complexes in solution, small or large. For a recent example, the SAXS model for a ~500-kDa RapA:RNA polymerase complex (~230 angstroms in its longest dimension), please see Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies.
ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation.
DISCUSSION - Crystal Structures
Mariusz Jaskolski: Pathological Behavior of Atomic Occupancy Factors
Mariusz Jaskolski: Geometrical Restraints of His Residues
M.Malinska, M.Dauter, M.Kowiel, M.Jaskolski, Z.Dauter (2015) Protonation and geometry of histidine rings. Acta Cryst. D71, 1444-1454.
This may be a good occasion to mention that for years Refmac has been using the older (1991) version (containing errors) of the Engh & Huber stereochemical dictionary, even though the authors themselves (E&H) corrected it in 2001...
ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography, Absorption 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 - Suggestions?
Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDB, PDB, PDBe,
Protein Geometry Database, Scattering
Programs: CCP4, COOT, DSSR, HKL, PHENIX, PyMOL, SOLVE, USF, XDS
Servers: ACHESYM, Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript,
Grade, PDBePISA, Phyre, Probity, 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)|