May. 10, 11:01:52 2013 Greetings, [ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ] The following checks were made on : ----------------------------------------- DISTANCES AND ANGLES We have checked your intra and intermolecular distances and angles with the procedures currently in place at PDB: ==> The following solvent molecules are further away than 3.5 Angstroms from macromolecule atoms which are available for hydrogen bonding in the asymmetric unit. none The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: none ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate Bond and Angle Parameters for X-ray protein structure refinement, Acta Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the dictionary values by more than six times this computed rms error is identified as an outlier. *** Covalent Bond Lengths: The RMS deviation for covalent bonds relative to the standard dictionary is 0.007 Angstroms The following table contains a list of the covalent bonds greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 Bond Dictionary Name ID Number Distance Value ------------------------------------------------------------------------ 0.044 PRO A 96 CG - CD 1.547 1.503 0.046 PRO B 96 CG - CD 1.549 1.503 -0.049 SER B 129 CA - C 1.476 1.525 -0.065 THR B 130 CA - CB 1.475 1.540 -0.045 VAL B 131 CA - CB 1.495 1.540 -0.047 VAL B 131 CB - CG1 1.474 1.521 -0.046 VAL B 131 CB - CG2 1.475 1.521 *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.3 degrees. The following table contains a list of the covalent bond angles greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Name ID Number Angle Value -------------------------------------------------------------------------------- -10.8 ILE A 30 N - CA - C 100.4 111.2 -8.6 ILE A 33 N - CA - C 102.6 111.2 9.4 GLY A 37 N - CA - C 121.9 112.5 -8.2 ILE A 40 N - CA - C 103.0 111.2 -9.9 ILE B 33 N - CA - C 101.3 111.2 9.3 SER B 72 N - CA - C 120.5 111.2 TORSION ANGLES The torsion angle distributions have been checked. The postscript file of the conformation rings showing the torsion angle distributions will be sent in a separate E-mail message. CHIRALITY The chirality has been checked and there are no incorrect carbon chiral centers. Some of O1P and O2P atoms do not follow the convention defined in the standard IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not indicate otherwise, we will switch the labels of O1P and O2P as shown below. OTHER IMPORTANT ISSUES ==> Please check carefully REMARKS 3 and 200 and fill in the parameters as appropriate. SEQUENCE WARNING: Residue (B SER 120 ) and Residue (B GLY 122 ) are not linked Distance of C-N bond is 3.56 HR5546A_XRay_em_bcr3.pdb: Error: Z value is 8. It should be 4.