JiaLabData |
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Freezer Stocks |
Cancer Project Details |
Main Plasmid Collection
BRI Plasmids Pichia strains E. coli strains
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Target Status (shows who is working on what, and their current progress) Cloning Information (protein size, expression trial information, etc) Source of Clones (IMAGE IDs and Genbank accession numbers of targets) |
Purification Protocols: |
Solution Recipes: |
Purification of GST-tagged proteins
from E. coli Purification of HIS-tagged proteins from E.coli Small-scale growth/purification of His/GST tagged proteins from E. coli (for expression trials, PDF, UPDATED) |
Terrific Broth (TB) Luria-Bertani Broth (LB) (Low Salt) LeMaster media (for selenomethione incorporation) YPD (for Pichia growth, NEW) 2X Laemlli SDS-PAGE Sample Buffer (NEW) SDS-PAGE and Western Blot solutions Agarose Gel Electrophoresis (includes TBE recipe and 6X DNA Loading Buffer recipes, NEW) |
Cloning Methods Jia Lab Cloning Manual (PDF) NEW, Work in progress Ligating a linker (annealled oligonucleotide) in to a plasmid (NEW) Ligation (of a cDNA clone in to a plasmid vector, NEW) |
E. coli manipulation methods Preparing Chemically Competent E. coli Transformation of E. coli by heat-shock (UPDATED) Plasmid Miniprep (alkaline lysis method, NEW) |
Crystallography Overview of x-ray data collection at Queen's home source Requirements for making a trip to BNL (Brookhaven National Laboratory) X8-C Beamline Parameters (NEW) |
Pichia methods: Electroporation of DNA in to Pichia (NEW) PCR screening of Pichia Small-scale purification of His-tagged proteins from Pichia
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Software and ScriptsClick on the program name to go to the software's website for instructions and other information ARP/wARP 6.0 command: "ccp4i" "A collection of disparate programs covering most of the
computations required for macromolecular crystallography". command: "cns < input.inp > output.out &" Our lab's most used program for refinement of models. "A
flexible multi-level hierachical approach for the most commonly
used algorithms in macromolecular structure determination.
including heavy atom searching, experimental phasing (including
MAD and MIR), density modification, crystallographic refinement
with maximum likelihood targets".
commands: "xdisp", "denzo", "scalepack", etc..
command: "eden"
command: "epmr cell.cel model.pdb data.hkl >
epmr.log &"
command: "hkl2000"
command: "hyss"
command: "molscript"
command: "dps"
command: "phaser < input.inp > output.out &"
command: "pymol"
commands: "render", etc..
command: "SnB" command: "sharp", or goto http://localhost:8080/ in web browser. A program using web browser interface for solving phases from MIR(AS), SIR(AS), SAD, and MAD data, as well as for density modification of electron maps.
commands: "shelxc", "shelxd", "shelxe", "shelxh",
"shelxl", "shelxpro", "shelxs", "shelxwat"
commands: "solve", "solve-huge", "resolve", "resolve_huge"
commands: "turbo"
commands: "xprep", "bigxprep"
commands: "xfit", "xtalmgr"
Cleanpdb.com
command: "cleanpdb.com < input.pdb >
output.pdb" Cns2fs
command: "cns2fsfour_linux" or
"cns2fsfour_sgi" then "cns_input.map xfit_output.map" Cns2xfit.awk
command: "cns2xfit.awk cns_input.coeff >
output.phs"
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