May. 10, 01:32:53 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 0.005 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 1.3 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 -------------------------------------------------------------------------------- -9.3 THR A 4 N - CA - C 101.9 111.2 -12.1 ALA A 45 N - CA - C 99.1 111.2 -7.9 VAL A 47 N - CA - C 103.3 111.2 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 ARG( A -89 ) ASP( A -88 ) PRO( A -87 ) THR( A -86 ) LEU( A -85 ) THR( A -84 ) LEU( A -83 ) SER( A -82 ) LEU( A -81 ) ILE( A -80 ) ALA( A -79 ) LYS( A -78 ) ASN( A -77 ) THR( A -76 ) PRO( A -75 ) ALA( A -74 ) ASN( A -73 ) SER( A -72 ) MSE( A -71 ) ILE( A -70 ) MSE( A -69 ) THR( A -68 ) LYS( A -67 ) LEU( A -66 ) PRO( A -65 ) SER( A -64 ) VAL( A -63 ) ARG( A -62 ) VAL( A -61 ) LYS( A -60 ) THR( A -59 ) GLU( A -58 ) GLY( A -57 ) TYR( A -56 ) ASN( A -55 ) PRO( A -54 ) SER( A -53 ) ILE( A -52 ) ASN( A -51 ) VAL( A -50 ) ASN( A -49 ) GLU( A -48 ) LEU( A -47 ) PHE( A -46 ) ALA( A -45 ) TYR( A -44 ) VAL( A -43 ) ASP( A -42 ) LEU( A -41 ) SER( A -40 ) GLY( A -39 ) SER( A -38 ) GLU( A -37 ) PRO( A -36 ) GLY( A -35 ) GLU( A -34 ) HIS( A -33 ) ASP( A -32 ) TYR( A -31 ) GLU( A -30 ) VAL( A -29 ) LYS( A -28 ) VAL( A -27 ) GLU( A -26 ) PRO( A -25 ) ILE( A -24 ) PRO( A -23 ) ASN( A -22 ) ILE( A -21 ) LYS( A -20 ) ILE( A -19 ) VAL( A -18 ) GLU( A -17 ) ILE( A -16 ) SER( A -15 ) PRO( A -14 ) ARG( A -13 ) VAL( A -12 ) VAL( A -11 ) THR( A -10 ) LEU( A -9 ) GLN( A -8 ) LEU( A -7 ) GLU( A -6 ) HIS( A -5 ) HIS( A -4 ) HIS( A -3 ) HIS( A -2 ) HIS( A -1 ) HIS( A 0 ) PDB Chain_ID: A 1 15 SEQRES: ARG ASP PRO THR LEU THR LEU SER LEU ILE ALA LYS ASN THR PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ALA ASN SER MSE ILE MSE THR LYS LEU PRO SER VAL ARG VAL LYS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU LEU PHE ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: TYR VAL ASP LEU SER GLY SER GLU PRO GLY GLU HIS ASP TYR GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: VAL LYS VAL GLU PRO ILE PRO ASN ILE LYS ILE VAL GLU ILE SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: PRO ARG VAL VAL THR LEU GLN LEU GLU HIS HIS HIS HIS HIS HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: ARG ASP PRO THR LEU THR LEU SER LEU ILE ALA LYS ASN THR PRO COORDS: ARG ASP PRO THR LEU THR LEU SER LEU ILE ALA LYS ASN THR PRO 1 15 106 120 SEQRES: ALA ASN SER MSE ILE MSE THR LYS LEU PRO SER VAL ARG VAL LYS COORDS: ALA ASN SER MSE ILE MSE THR LYS LEU PRO SER VAL ARG VAL LYS 16 30 121 135 SEQRES: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU LEU PHE ALA COORDS: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU LEU PHE ALA 31 45 136 150 SEQRES: TYR VAL ASP LEU SER GLY SER GLU PRO GLY GLU HIS ASP TYR GLU COORDS: TYR VAL ASP LEU SER GLY SER GLU PRO GLY GLU HIS ASP TYR GLU 46 60 151 165 SEQRES: VAL LYS VAL GLU PRO ILE PRO ASN ILE LYS ILE VAL GLU ILE SER COORDS: VAL LYS VAL GLU PRO ILE PRO ASN ILE LYS ILE VAL GLU ILE SER 61 75 166 176 SEQRES: PRO ARG VAL VAL THR LEU GLN LEU GLU HIS HIS COORDS: PRO ARG VAL VAL THR LEU GLN LEU GLU HIS HIS 76 86 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS GLU( A 42) CB CG CD OE1 OE2