100 Years of X-ray Crystallography (IYCr2014)
1: Bird GH, Irimia A, Ofek G, Kwong PD, Wilson IA, Walensky LD. Stapled HIV-1
AND TRICKS -
Effect of PEG
I had one case where PEG4000 grown crystals would be resistant to dissolving and would easily bend; the thinner rods would spring back staight. After placing the crystals into buffer known to dissolve them, I poked the crystals hard and the insides squeezed out like toothpaste, leaving an empty sack behind. the bottom-line is that fresh crystals diffracted better than old crystals because of this cross-linking.
Suggestions: (1) Make your PEG stocks up fresh or store them in the freezer as aliquots; (2) Remove oxidized PEGs from your stocks (See Ray et al. Biochemistry, 30, 6866-6875, 1991 and Jurnak, J. Cryst. Growth, 76, 577-582, 1986); (3) Check to see if freshly grown crystals behave better.
ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation.
for Refinement and Deposition/Publication
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Xinhua Ji (NCI): Concluding Remarks - During our discussion, I also consulted with the instructors and lecturers of the Cold Spring Harbor Laboratory 2014 course X-ray Method in Structural Biology. Taken together, the following are recommended: (1) A single date set should be used for structure solution, refinement, and deposition; (2) For the highest resolution (outmost) shell, the I/s(I) value should be > 1.0 and the completeness should be > 50%; and (3) At the claimed resolution of the structure, the overall completeness should be > 93% and the completeness for the outmost shell should be > 70% as shown in the table below.
*Value to be tested and optimized.
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.
AND TUTORIALS NEW ADDITION - Structure Factor
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 BY KEVIN COWTAN (2014)
- NEW ADDITION - Protein Geometry
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: 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)|