Foster Group Protocols

Ross's quiche recipe! 

Laboratory

Sample Preparation

Sample dilution calculator [GNUMERIC (Preferred format)]
Dialysis analysis and planning [GNUMERIC (Preferred format)]
How to make Trp stock [TXT]

Buffer recipe calculator

Clicky

Buffers: pH changes with temperature

Spreadsheet for calculating correlation between pH and temprature 
Table of buffer constants (needed to apply above spreadsheet to your buffer) 

Scientific Method

Propagation of experimental errors
Effect of Heat Capacity on delta-G

Molecular/Micro Biology

QuikChange site-directed mutagenesis
Preparation of chemically competent cells
Preparation of electroporation competent cells.
Transformation of BL21(DE3) cells for protein expression
Double transformation of BL21(DE3) cells for protein expression
Elution of Purified DNA off Agarose
Minimal Media Recipe for E. coli expression of labeled proteins
Expression of proteins in minimal media for preparation of ¹⁵N or ¹³C/¹⁵N labeled samples
Removal of Trp from B. staerothermophilus TRAP
Growth media and conditions for Mth
Preparation of Synthetic RNA Samples for NMR

Protein Purification

Pfu Pop5
Pfu p30 (MBP fusion)
Mth proteins: p21, p29, p30, and Pop5
T7 RNA Polymerase
Bsu formyl Anti-TRAP
Refolding C65 from Inclusion bodies
Trypsin digestion of C170 l-Int
Expression and purification of PDF-Tr in minimal media for NMR or Spectroscopic studies (Co²⁺)
Expression and purification of C170-l-Intfor NMR studies

Chromatography

GE Life Sciences Chromatography 
Routine use of the HPLC
Routine use of the FPLC
GST pull-down/binding assay
Ni-affinity (HiTrap columns)

Crystallography

Optimization screen calculator for 24-well trays

Instrumentation

Isothermal Titration Calorimetry (Updated 2010/07/07)

Instrumentation web page (Click on ITC)

Fluoromax

Fluoromax 3: Trp-TRAP assay [TXT]

Mass spectrometry (Updated 2010/07/27)

MALDI-MS protocol (Kleckner) [ODT]

Stopped-flow

Stopped-flow experimental design [GNUMERIC (Preferred format)]

Stopped-flow Trp-TRAP assay [TXT]

Stopped-flow diagram 1, Stopped-sflow diagram 2, Stopped-flow diagram 3

UV-vis spec

Determining concentration via UV absorbance

SAXS

SAXS tutorial documentation (Ian Kleckner)

SAXS tutorial presentation (Ian Kleckner)

Putnam et al. (2007)

tab/SAXS processing scripts (tarball)

Structure Probing

Invitrogen Molecular Probes Handbook

Services

DNA Sequencing at PMGF 
OSU Fermentation Lab 

NMR

Data Collection

Assorted pulse programming tips
Using the shaped-pulse tool
NMR calendars 
NMR time request form 
Tutorial to collect ¹H¹⁵N 2D spectrum
Log sheet for multiple NMR experiments
DOSY protocol
Measuring ¹H pulses
Measuring ¹³C pulses
Measuring ¹⁵N pulses
Measuring ²H pulses
Measuring ²H₂O splittings
Tuning and Shimming
Calibrating probe temperature
Using reduced volume Shigemi tubes
Setting up 15N relxation experiments
Backing up your data

Data Processing and Analysis

Get files from NMR computers (Kleckner, 2010/09/23) [PDF]
Process 1D spectra (Foster, 2010/05/17) [PDF]
NMR referencing [TXT]
NMR Reference Calculator
IUPAC Recommendations for the presentation of NMR structures of proteins and nucleic acids (PDF)
NMRPipe Tutorials
NMRPipe installation instructions
Calibrating chemical shifts
Using NMRview to assign NOEs
Iterative structure calculations
Setting up an xplor input
Calculating RDCs by comparing aligned/unaligned spectra
Converting data to NMRPipe format
Extracting 1D Vectors from nD NMRPipe data
Setting up Aria
List of awk, shell and other scripts (see Mark) (Scripts Dir)

Modelling

Pymol tutorial: terminology & commands 
IntroductionToPyMOL-091005 (Delano Scientific), zipped file
Mapping chemical shift perurbations in PyMol
Mapping Chemical Shift Perturbations onto Backbone Using GRASP
AWK macro to map residue property to CA atom radius in MOLMOL
Tips and Scripts to work w/ CNS files, MOLMOL and NMRVIEW.

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Writing reports and papers