Quick input guide: tutorial 4

Rigid-body Refinement of a Molecular Replacement model

This tutorial has been run in the "Standard" user level. In this mode, default values are used for most of the input items. The ones that needed some extra attention are described below:

Input item	Notes
Partial Structure	The PDB file with the PP Molecular Replacement solution. XYZ's for these atoms will be refined by BUSTER-TNT.
Chemical composition	The chemical composition was computed from the missing residues, but you could also try declaring: say 10 N atoms (or C, or O) for each of the 149+61=210 missing residues in the a.u.; one O atom for each of the (326+149)=475 residues of the complex, to mimic ordered water molecules; the missing atoms are given a B of 35, much higher than the average B of the atoms in the partial model (18).
Missing atoms prior envelope	From current phases. The current 2Fo-Fc map is used to define the regions where the missing atoms are expected to be - based on the declared solvent content.
Solvent content	0.40: this estimate is based on the nominal (326+149)=475 residues in the asymmetric unit
TNT sequence file	It was prepared with the script $BDG_home/bin/buster/pirToSeq.pl starting from the ASCII 1-letter sequence files for PP and PI-3. The script first run to obtain the TNT sequence file for PP; then it was run for PI-3 and the PI-3 sequence file was appended to the one for PP. The six disulphide bonds were added editing the file by hand - and so was the bond from Ser A68 to its phosphate group (phosphoserine). At a later stage the MPD ligand was added.
Weight on the x-rays residual	Set to 3.5 - a value low enough to keep a fairly tight stereochemistry.
Stereochemical restraints libraries	$BDG_tntdata/csdx_protgeo.dat: geometry of standard amino-acids $BDG_tntdata/bcorrel.dat: temperature factors correlation restraints for standard amino-acids $BDG_tntdata/contact.dat: basic non-bonded distances for most commonly occurring atom types Three more dictionaries are included that will only be used at later stages of refinement when the ligands will be built: $BDG_datafiles/PSE.tnt.dat: the dictionary with the linkage from serine to phosphate, and the phosphate geometry; $BDG_datafiles/MPD.tnt.dat: the dictionary for 2-methyl-2,4-pentanediol (MPD) $BDG_datafiles/PP_PI-3.exclude.dat: this file allows inclusion in the model of a water molecule sitting on the twofold axis: EXCLUDE W|76:O W|76:O CONSTANT XYZ W|76:O