This tutorial originally comes from the Phaser Wiki.

Download the data from 6_mr_sad.tgz

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MR/SAD

This tutorial illustrates a common molecular replacement/experimental phasing scenario, when refinement is hindered by very strong model bias, but there is some experimental phasing signal available.

Goat α-lactalbumin is 45% identical to hen egg-white lysozyme. Although it is possible to solve lysozyme using α-lactalbumin as a model, it is very difficult to refine the structure, partly because of model bias. Unfortunately, the low solvent content of this crystal form limits the ability of density modification to remove the bias. However, one can use anomalous scattering from intrinsic sulfur atoms to improve phases dramatically. It is noteworthy that the anomalous signal from the sulfur atoms is not sufficient for ab initio phasing (it is not possible to locate the anomalous scatterers from the data alone).

1. Solve the structure by MR with the α-lactalbumin model. Please note that if you used Molrep for this you will need to follow by refinement with Refmac in order to produce an MTZ file with phases.
2. For a fairer comparison of phase quality, we will treat the molecular replacement solution as a source of experimental phase information. (If you use the automated model building starting from PDB file mode, the current version of ARP/wARP will be able to build the structure, but older versions coupled with older versions of Refmac5 failed.) Do a quick solvent flattening with Parrot (choose Use PHI/FOM instead of HL coefficients because the MTZ file produced after MR doesn't include Hendrickson-Lattman coefficients; set PHI=PHIC and FOM=FOM. You should also select Use map coefficients, then set F=FWT and PHI=PHWT). This sets the map used in the first cycle of density modification, rather than calculating it from FP and PHI/FOM.
3. Start up ARP/wARP Classic in automated model building starting from experimental phases mode. Select the MTZ file from Parrot. To start from the Parrot map, select Use a different (pre-weighted) Fobs for initial map calculation under the ARP/wARP flow parameters folder, then set FBEST=parrot.F_phi.F, PHIB=parrot.F_phi.phi and FOM=Unassigned. Select the sequence file, and note there are 129 residues in lysozyme. To save time, do 3 cycles of autobuilding instead of 10.
4. Now add the S-SAD phase information.
   • Bring up the GUI for the Phaser SAD pipeline in the Automated Search & Phasing section of the Experimental Phasing module.
   • Fill in all of the yellow boxes.
   • Set Mode for experimental phasing to SAD with molecular replacement partial structure
   • Uncheck the Parrot and Buccaneer steps of the pipeline (to allow control for better comparison with the MR model alone).
   • Under the Define atoms heading, set LLG-map completion to on: select atom types and Complete with atom type to S
   • Also set Partial structure input as to the molecular replacement solution (output PDB-file) you have obtained in the first step.
5. Run Phaser after you entered all the information.
6. Solvent flatten with Parrot using a similar protocol to step 2. However, you should not choose Use PHI/FOM instead of HL coefficients. Choose the HLanomA/B/C/D coefficients because these describe the phase information obtained only from the anomalous scattering information and not from the molecular replacement model; using HLA/B/C/D would include the model phase information, which would bias maps from subsequent cycles of phase improvement to look like the model.
7. Run ARP/wARP using a similar protocol as in step 3, except you should open the Refmac parameters folder and choose the option to include HL phase restraints. In the MTZ data section, set HLA/HLB/HLC/HLD to the HLanomA/B/C/D coefficients.

Questions

1. How many anomalous scatterers has Phaser found? Check them against the model and guess what they may be! Why is it not important to specify the exact element type in this case?
2. If you did not know the correct space group (from the MR step), would you have to run Phaser SAD-phasing twice?
3. Compare the two ARP/wARP runs! Which one has built more residues?