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PROTEIN STRUCTURE VALIDATION NOTE: The coordinates file needs to be in Brookhaven format and the structure factor file in mmCIF format and the resolution in Angstrom. PROCHECK v.3.5.4 PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. Coordinate file : Resolution: SFCHECK v.4.0(CCP4 version) SFCHECK evaluates the structure-factor data obtained from X-ray diffraction experiments and assesses the agreement of the atomic coordinates with these data. Coordinate file : Structure factor file: PROVE v.2.5.1 The atomic volume check (done by the PROVE program) calculates for each atom in the structure the atomic volume. It compares these volumes with a pre-computed average for each atom type. This comparison results in a Z-value for each buried atom. A structural Zrms is also calculated, using the square of these scores. Coordinate file : Options:   -rad  -dna  -het  -hoh                   -res (resolution):                   -rprobe (radius):  ERRAT ERRAT is a protein structure verification algorithm that is especially well-suited for evaluating the progress of crystallographic model building and refinement. The program works by analyzing the statistics of non-bonded interactions between different atom types. Coordinate file : WASP This program will take a Protein Data Bank structural file with solvent electron density peaks designated as water oxygens. Based on simple structural criteria it will pick out the peaks that could be metal ions (Na+, Li+, Mg++, Ca++). The chosen peaks are subsequently written to 4 pdb-formatted files one for each ion. The temperature factor field is replaced by the calculated ion-specific valence of that solvent peak. Coordinate file : Scaling factor for Vdw radii (0.8-0.9): Ligation destance (3.4-4.0): % nominal valence required for output (0.75-1.0): DDQ V2.0 NOTE: To run DDQ, the PDB file must contain SCALE information. DDQ is a program written to aid as a tool in the automatic assessment of the local and global accuracy of macromolecular crystal structures as well as assessing whether crystallographic refinement has been completed satisfactorily. DDQ is especially meant for structures which benefit from a high local accuracy such as targets for rational drug design. Coordinate file : The file containing the positive difference peaks generated by CNS : The file containing the negative difference peaks generated by CNS : WHATCHECK v.19991018-1516 WHATCHECK is a subset of WHATIF program. Coordinate file : Any questions, comments? Please email <wangx@sdsc.edu>.

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