Suggested Reading/Viewing Materials:
     1) Pre Crystallization Lab Video
     2) What a crystallographer should know about a protein before beginning crystallization trials by Michael Sawaya.
     3) Heavy Atom Safety, Selection, and Screening by Michael Sawaya (2000).
     4) Screening for Phasing Atoms in Protein Crystallography by Boggon & Shapiro (2000).
Experiments Performed in Lab:
     1) Crystallization of Proteinase K and complex with PMSF
     2) Heavy Atom Derivative Screening by Native Gel Electrophoresis
     3) Preparation of Heavy Atom derivatives 

Suggested Reading Materials:
     1) Data Collection Strategies by Zbigniew Dauter (1999).
     2) Solvent Content of Protein Crystals by B.W. Matthews (1968).
Activities In Lab:
     1) Cryo-crystallographic technique video (WMV file 65 Mb, open with Windows Media Player)
     2) Practice removing and storing crystals for synchrotron trip
     3) Initiate data collection

Suggested Reading Materials:
     1) Chapter 6 (page 101-127) from Crystallography Made Crystal Clear by Gale Rhodes.
Activities in Lab:
     1) Familiarization with simple Unix commands.
     2) Calculation of isomorphous and anomalous difference Patterson maps.
Assignments: Patterson reports completed in lab
 

Suggested Reading Materials:
     1) Chapter 6 (page 101-127) from Crystallography Made Crystal Clear by Gale Rhodes.
Activities in Lab: 
     1) Phasing with Shelx and HKL2MAP
     2) Solvent Flattening
     3) Chose correct handedness
     4) Calculate electron density
     5) View density with "COOT"
Assignments:  Phasing reports completed in lab

Suggested Reading Materials:
     1) Electron density map intepretation by T. A. Jones and M. Kjeldgaard.
Activities in Lab:
     1) Placing Alpha helices and beta strands in density.
     2) Assigning protein sequence to density
     3) Run & evaluate automatic chain tracing program
Assignments:  Complete building an atomic model of Proteinase K by March 2-6, 2026. Sooner is better.
 

Suggested Reading Materials:
     1) T12 manual
     2) Sample Preparation protocol
Activities in Lab:
     1) Preparation of biological samples for negative stain TEM.
     2) Basic operating procedures for loading a viewing a sample on a T12 electron microscope

Suggested Reading Materials:
     1) CryoSPARC tutorial
Activities in Lab:
     1) Motion Correction of CryoEM images
     2) Contrast Transfer function (CTF) Estimation
     3) Particle Picking and Extraction
     4) 2D classification
     5) Ab initio 3D reconstruction
     6) Homogeneous refinement

Suggested Reading Materials:
     1) None yet.
Activities in Lab:
     1) Calculation of difference Fourier electron density maps.
     2) Evaluation of maps
     3) Refinement of Structure
     4) Run Procheck, Verify3D and Errat
Assignments:  Final structure reports completed in lab
 

Suggested Reading Materials:
     1) Talos tutorial
Activities in Lab:
     1) Load microcrystals in Talos microscope
     2) View and select a microcrystal of interest
     3) Collect diffraction data as a tilt series of ~70 degrees
     4) Process diffaction data with XDS
     5) Solve phase problem using direct methods
     6) Observe atomic structure