| Newsletter No. 400
|| June 17, 2019
|Michael Rossmann, 88
ACA 2019, FEBS 2019, Protein Society 2019
| TIPS, TRICKS, METHODS - Date Collection with ID22 and Eiger16M
Fred Dyda (NIDDK): Last week we collected ID data at 50 ms / 0.2 degrees at 30% transmission. With these, 180 degree of data took only 45 s.
This suggests that one could go faster with wider frames and/or higher transmission.
John says that the limit in exposure time is 20 ms. This is where the stream server stars to choke in spitting out the .cbf files from the stream.
Fred Dyda (NIDDK): During a survey of data collection practices, it became apparent that most users do not take advantage of the current capabilities of ID22 and the Eiger16M. In particular it has been shown that excellent data can collected using 0.2 or 0.25 degrees / 0.05 sec speed so 200 degrees can be collected in 36 or 50 sec. One would of course have to increase transmission, but this should be possible as most people seem to collect at 80 or 90% attenuation. This should be OK, as all indicate that decay is dependent of totla accumulated does and is independent of dose rate.
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.
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 - Data Collection Strategies
The Fascinating World of 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)|