May. 10, 16:48:01 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 0.006 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.0 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 -------------------------------------------------------------------------------- -6.1 LEU A 55 N - CA - C 105.1 111.2 7.7 PHE A 75 N - CA - C 118.9 111.2 -8.6 VAL A 76 N - CA - C 102.6 111.2 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. ==> The following residues are missing: (Note: The SEQ number starts from 1 for each chain according to SEQRES sequence record.) RES MOD#C SEQ MET( A -99 ) THR( A -98 ) SER( A -97 ) THR( A -96 ) PHE( A -95 ) ASP( A -94 ) ARG( A -93 ) VAL( A -92 ) ALA( A -91 ) THR( A -90 ) ILE( A -89 ) ILE( A -88 ) ALA( A -87 ) GLU( A -86 ) THR( A -85 ) CYS( A -84 ) ASP( A -83 ) ILE( A -82 ) PRO( A -81 ) ARG( A -80 ) GLU( A -79 ) THR( A -78 ) ILE( A -77 ) THR( A -76 ) PRO( A -75 ) GLU( A -74 ) SER( A -73 ) HIS( A -72 ) ALA( A -71 ) ILE( A -70 ) ASP( A -69 ) ASP( A -68 ) LEU( A -67 ) GLY( A -66 ) ILE( A -65 ) ASP( A -64 ) SER( A -63 ) LEU( A -62 ) ASP( A -61 ) PHE( A -60 ) LEU( A -59 ) ASP( A -58 ) ILE( A -57 ) ALA( A -56 ) PHE( A -55 ) ALA( A -54 ) ILE( A -53 ) ASP( A -52 ) LYS( A -51 ) ALA( A -50 ) PHE( A -49 ) GLY( A -48 ) ILE( A -47 ) LYS( A -46 ) LEU( A -45 ) PRO( A -44 ) LEU( A -43 ) GLU( A -42 ) LYS( A -41 ) TRP( A -40 ) THR( A -39 ) GLN( A -38 ) GLU( A -37 ) VAL( A -36 ) ASN( A -35 ) ASP( A -34 ) GLY( A -33 ) LYS( A -32 ) ALA( A -31 ) THR( A -30 ) THR( A -29 ) GLU( A -28 ) GLN( A -27 ) TYR( A -26 ) PHE( A -25 ) VAL( A -24 ) LEU( A -23 ) LYS( A -22 ) ASN( A -21 ) LEU( A -20 ) ALA( A -19 ) ALA( A -18 ) ARG( A -17 ) ILE( A -16 ) ASP( A -15 ) GLU( A -14 ) LEU( A -13 ) VAL( A -12 ) ALA( A -11 ) ALA( A -10 ) LYS( A -9 ) GLY( A -8 ) ALA( A -7 ) LEU( A -6 ) GLU( A -5 ) HIS( A -4 ) HIS( A -3 ) HIS( A -2 ) HIS( A -1 ) HIS( A 0 ) HIS( A 1 ) PDB Chain_ID: A 1 15 SEQRES: MET THR SER THR PHE ASP ARG VAL ALA THR ILE ILE ALA GLU THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: CYS ASP ILE PRO ARG GLU THR ILE THR PRO GLU SER HIS ALA ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: ASP ASP LEU GLY ILE ASP SER LEU ASP PHE LEU ASP ILE ALA PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: ALA ILE ASP LYS ALA PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: THR GLN GLU VAL ASN ASP GLY LYS ALA THR THR GLU GLN TYR PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: VAL LEU LYS ASN LEU ALA ALA ARG ILE ASP GLU LEU VAL ALA ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: LYS GLY ALA LEU GLU HIS HIS HIS HIS HIS HIS THR SER THR PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... THR SER THR PHE 2 5 106 120 SEQRES: ASP ARG VAL ALA THR ILE ILE ALA GLU THR CYS ASP ILE PRO ARG COORDS: ASP ARG VAL ALA THR ILE ILE ALA GLU THR CYS ASP ILE PRO ARG 6 20 121 135 SEQRES: GLU THR ILE THR PRO GLU SER HIS ALA ILE ASP ASP LEU GLY ILE COORDS: GLU THR ILE THR PRO GLU SER HIS ALA ILE ASP ASP LEU GLY ILE 21 35 136 150 SEQRES: ASP SER LEU ASP PHE LEU ASP ILE ALA PHE ALA ILE ASP LYS ALA COORDS: ASP SER LEU ASP PHE LEU ASP ILE ALA PHE ALA ILE ASP LYS ALA 36 50 151 165 SEQRES: PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP THR GLN GLU VAL ASN COORDS: PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP THR GLN GLU VAL ASN 51 65 166 180 SEQRES: ASP GLY LYS ALA THR THR GLU GLN TYR PHE VAL LEU LYS ASN LEU COORDS: ASP GLY LYS ALA THR THR GLU GLN TYR PHE VAL LEU LYS ASN LEU 66 80 181 195 SEQRES: ALA ALA ARG ILE ASP GLU LEU VAL ALA ALA LYS GLY ALA LEU GLU COORDS: ALA ALA ARG ILE ASP GLU LEU VAL ALA ALA LYS GLY ALA LEU GLU 81 95