South African Structural Biology Initiative

Documentation and Protocols

Online courses

• Electron Microscopy for Biologists
• Structural Biology Moodle site - an online course management system with lectures for third year students, honours students and masters students.

Software and Equipment Manuals:

Spider Documentation | "O" | Pymol | Electron Microscopes

Spider Documentation

• Contents
• Overview & Licensing
• Operation Changes
• Current News & Bugs
• Getting Started
• Philosophy Of The Single Particle Approach
• User's Guide
• Quick Start Guide To Spider
• Tutorial
• Operations Listing
• Cross-Referenced Operations Listing
• Techniques
• Other Documentation
• FAQ
• Data File Format
• Web (Graphics Interface For Spider)
• Installation
• Release Notes
• Computer Use Tips (At Albany)
• Sample Reconstructions (VRML Format)
• RVBC (Resource For Visualization Of Biological Complexity)
• Sterecon (Stereo Contour Reconstruction System For Microscopy Data)
• Some Relevant WWW Sites

"O"

• O Protocol

Pymol

• Reference Manual
• User Manual

Electron Microscope Manuals

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Structural biology Protein Preparation protocols

| Before you begin | Biochemistry & Assays | Crystallography | Electrophoresis & gel staining | Immunoassays & other Immunological Techniques | Liquid Handling | Protein Expression, Cloning & Biotechnology Techniques | Protein Purification | Spectrophotometry & UV detection |

• Before You Begin
  • General Notes
  • Designing of buffers
  • Expressing concentration and dilution of stocks
  • General Molecular Lab Skills and Techniques - By Joni Frederick
  • QIAGEN^® Bench Guide
• Biochemistry and Assays
  • The BCA Assay
  • The Bradford Assay
  • The Lowry Assay
  • Nitrilase activity assay
  • Ultraviolet Absorbance of Aromatic Amino Acids
• Crystallography
  • Journal article: Introduction to general crystallography
• Electrophoresis and gel staining
  • Agarose gel electroporesis
  • SDS-PAGE
  • ProteoSilver™: High Sensitivity Silver Stain for SDS-PAGE
  • Journal article: Imidazole–SDS–zinc reverse staining
  • See also: Gel electrophoresis/SDS-PAGE in our postgraduate content
• Immunoassays and other Immunological Techniques
  • Antibody Purification
  • Chicken immunoglobulin preparation
  • Dot blot assays
  • Western blot
• Liquid Handling
  • Decontamination Procedures for Gilson Pipettes
  • Gilson Manual Liquid Handling Catalogue (2004)
  • Gilson Pipetman® Two Minute Inspection
  • Pipetman® P User Manual
  • Pipetman® Ultra Multichannel Brochure
  • Verification Procedure for Accuracy and Precision
• Protein Expression, Cloning and Biotechnology Techniques
  • Alkaline Lysis
  • Bacterial Growth Media and Solutions
  • Glycerol stocks of transformed cells
  • Growth and Induction of Cells
  • Journal article: Secreted bacterial proteins
  • Journal article: Applications of yeast in biotechnology
  • Journal article: Construction and deconstruction of bacterial inclusion bodies
  • Journal article: Protein aggregation as bacterial inclusion bodies is reversible
  • Journal article: Recombinant protein expression in Escherichia coli
  • Journal article: Ultrasonication of E. coli cells
  • Lysis of E. coli cells
  • Promega Subcloning Notebook
  • The Recombinant Protein Handbook
  • Transformation of plasmid DNA to competent E. coli cells
• Protein Purification
  • Protein Purification
  • Protein Purification - An Overview
  • Chromatography
    • Chromatography in Protein purification
    • Affinity Chromatography
      • Affinity Chromatography - Principles and Methods
      • Affinity Chromatography - Overview
      • Coupling to pre-activated gels
      • Amersham HiTrap™ Blue HP Affinity Columns
      • Purification of (His)6-tagged proteins
      • Reactive dye affinity chromatography matrices
    • Gel filtration chromatography
      • Gel filtration chromatography - Principles and methods
      • Gel filtration chromatography - overview
      • Desalting and buffer exchange with Sephadex^® G-25
      • Sephacryl high resolution media
      • Instructions for the use of Sephacryl high resolution media
      • Polymer-based TSK-GEL TW and TSK-GEL PW_XL columns
    • High Pressure Liquid Chromatography (HPLC)
      • Gilson Instruments
        • Gilson UniPoint™ System Software User Guide
        • 305/306 HPLC Pumps (Technical Specifications)
        • 305 Piston Pump User's Guide
        • Flow rate guide
        • Gilson FC 203B Fraction Collector User's Guide
        • Gilson FC 203B Fraction Collector Quick Reference Guide
        • Minipuls 3 Peristaltic Pump User’s Guide
        • SC-type Piston Pump Heads User’s Guide
        • Selecting Tubing & Connectors for Minipuls 3 Peristaltic Pump
        • Tubing Properties
    • Hydrophobic Interaction Chromatography
      • Principles and Methods
      • Hydrophobic Interaction Chromatography
    • Ion-exchange chromatography
      • IEX - Principles and methods
      • IEX & chromatofocusing - Principles and methods
      • Ion Exchange Chromatograhy
      • ANX Sepharose 4 Fast Flow (high sub) INSTRUCTIONS
      • ANX Sepharose 4 Fast Flow (high sub) INFORMATION
      • CM, DEAE, Q and SP Sepharose Fast Flow ion exchangers
      • HiPrep 16/10 Q FF, SP FF and ANX FF (high sub) prepacked columns
      • HiTrap ion exchange columns
      • HiPrep 16/10 CM FF and DEAE FF prepacked ion-exchange columns
      • HiPrep 16/10 SP XL and Q XL prepacked ion-exchange columns
      • Q Sepharose® XL and SP Sepharose® XL anion exchangers
      • Q Sepharose XL, Q Sepharose XL virus and SP Sepharose XL
      • Q Sepharose Fast Flow anion exchanger
    • Reversed Phase Chromatography
      • Reversed Phase Chromatography - J Brewer, 1998
    • Other Chromatography Equipment
      • All about fittings. John W Watts
      • Column K 9
      • Superdex columns
      • HR 16/5, HR 16/10, HR 16/50 columns. John W Watts
      • Amersham C Columns for Standard Chromatography (Columns C10, C16, C26)
      • Amersham C Column Adaptors (Adaptors AC 10, AC 16, AC 26)
      • Amersham C Column Packing Reservoirs (Reservoirs RC 10, RC 16, RC 26)
      • Instructions for XK-columns and AK-adaptors
      • Rheodyne injectors. Rheodyne
  • Ultrafiltration
    • Desalting and Buffer Exchange with Millipore Centrifugal Devices
  • Methods for Concentrating Protein Solutions
• Spectrophotometry and UV detection
  • Gilson 151/152 UV/VIS Detectors User’s Guide
  • Gilson 155/156 UV/VIS Detectors User’s Guide
  • Probing Protein Structure by Spectroscopy
  • ThermoSpectronic (Spectrophotometer Instrument Manual)

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