Overview of MR in CCP4 II

1. Overview of MR in CCP4 II

2. Roadmap http://www.ccp4.ac.uk/dist/ccp4i/help/roadmaps/

3. Information On Molecular Replacement • CCP4 Study Weekend Proceedings 2001 • Acta D57 October 2001 Part 10 • http://www.ccp4.ac.uk/dist/examples/tutorial2000/html/

4. CCP4 Programs Used In MR • almn - calculates rotation function overlap values using FFT techniques (alternative to AMORE) • amore - Jorge Navaza's state-of-the-art molecular replacement package • beast - Likelihood-based molecular replacement • ecalc - calculate normalised structure amplitudes • fsearch - 6-d molecular replacement (envelope) search • getax - real space correlation search • molrep - automated program for molecular replacement • polarrfn - fast rotation function which works in polar angles • rfcorr - Analysis of correlations between cross- and self-Rotation functions • rotmat - interconverts CCP4/MERLOT/X-PLOR rotation angles • rsearch - R-factor and correlation coefficient between Fcalc and Fobs • tffc - Translation Function Fourier Coefficients

5. Estimating The NO of Molecules in ASU Most protein crystals contain about 50% water. The number of protein molecules in the asymmetric unit of a crystal can be estimated with Matthews_coef. Biochemical data is also important. Vm = cell volume ( cubic As) V ----------------------- = --- M*nasymu*nmols_asu M*Z M = molecular weight of protein in daltons V = volume of unit cell. Z = no. of molecules in unit cell. = nasymu*nmols_asu nasymu = number of asymm. units nmols_asu = number of molecules in asym unit.

6. Matthews_coef 1. 2.

7. Analyse Data For MR Look at the Experimental Data You should do two things: a) Create a Patterson map and search it for peaks. We expect a big peak at the origin (position 0,0,0) but if there is another big peak (perhaps about 0.25 the size of the origin peak) then perhaps there is translation between the molecules in the asymmetric unit and it will be more difficult to solve. (The theory behind this is explained on the web site of Bernhard Rupp: http://www-structure.llnl.gov/xray/101index.html For more information, go to the section on Phasing Techniques on this website, and click on NCS with native Patterson maps) b) Create a Wilson plot which is an indication of the self consistency of the data. Also find the average B-value of the data - this can be used to help the molecular replacement program.

8. Analyse Data for MR II

9. Analyse Data For MR III Wilson Plot Compare Model and Data Bfactors If they differ greatly you will need correcting BADD value in amore

10. Main Molecular Replacement Programs AMoRe: Jorge Navaza's state-of-the-art molecular replacement package ActaD D57 p1367 MOLREP: automated program for molecular replacement ActaD D57 p1451 BEAST: Likelihood-based molecular replacement ActaD D57 p1373

11. AMoRe : Model Database Currently only AMoRe has this functionality.

12. AMoRe : Main Window

13. AMoRe : Choosing a procedure Choose the procedure you want to follow

14. AMoRe: Parameters Choose the model to use MTZ file (line beneath is equivalent to LABIN)

15. AMoRe : Key Parameters Space Group Choice Resolution Range

16. AMoRe: Output Files Http://www.ccp4.ac.uk/dist/ccp4i/help/modules/molrepl.html#solution_files

17. AMoRe: Output Files II CC between Fs and Is Euler Angles Fractional Shift RFactor

18. AMoRe: Memory?

19. AMoRe: Other Utils Amore Model Database Amore Main Window Edit Amore Solution File Build Amore Output Model

20. MOLREP: Main Window

21. MOLREP: Main Widow II Values for Translational NCS automatically put in if XML enabled from Preferences.

22. BEAST

23. BEAST : Main Window II Fraction of target represented by model BEAST is a slow procedure but has proven successful in some difficult cases.

24. Comparative Times