Overview of MR in CCP4 II

Roadmap

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

Information On Molecular Replacement

CCP4 Study Weekend Proceedings 2001Acta D57 October 2001 Part 10

http://www.ccp4.ac.uk/dist/examples/tutorial2000/html/

CCP4 Programs Used In MRalmn - 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

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.

Matthews_coef

1.2.

Analyse Data For MRLook 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.

Analyse Data for MR II

Analyse Data For MR III

Wilson Plot

Compare Model and Data Bfactors

If they differ greatly youwill need correcting BADD value in amore

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

AMoRe : Model Database

Currently only AMoRe has this functionality.

AMoRe : Main Window

AMoRe : Choosing a procedure

Choose the procedureyou want to follow

AMoRe: ParametersChoose the model to use

MTZ file (line beneath is equivalent to LABIN)

AMoRe : Key Parameters

Resolution Range Space Group Choice

AMoRe: Output Files

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

AMoRe: Output Files IIEuler Angles Fractional

Shift

RFactor

CC between Fs and Is

AMoRe: Memory?

AMoRe: Other Utils

Amore Model Database

Amore Main Window

Edit Amore Solution File

Build Amore Output Model

MOLREP: Main Window

MOLREP: Main Widow II

Values for Translational NCS automaticallyput in if XML enabled from Preferences.

BEAST

BEAST : Main Window II

BEAST is a slow procedure but has proven successful insome difficult cases.

Fraction of target represented by model

Comparative Times

Amore 30 seconds

MOLREP 3 min

Beast