May. 11, 01:43:25 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 1.1 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 -------------------------------------------------------------------------------- -7.5 VAL A 52 N - CA - C 103.7 111.2 -9.4 ASN A 67 N - CA - C 101.8 111.2 6.9 LYS A 90 N - CA - C 118.1 111.2 -11.6 PHE A 95 N - CA - C 99.6 111.2 6.9 SER A 96 N - CA - C 118.1 111.2 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 MSE( A-104 ) VAL( A-103 ) ASN( A-102 ) PHE( A-101 ) LYS( A-100 ) ASP( A -99 ) LYS( A -98 ) SER( A -97 ) MSE( A -96 ) PRO( A -95 ) THR( A -94 ) ALA( A -93 ) ILE( A -92 ) GLU( A -91 ) LYS( A -90 ) ALA( A -89 ) LEU( A -88 ) ASP( A -87 ) PHE( A -86 ) ILE( A -85 ) GLY( A -84 ) GLY( A -83 ) MSE( A -82 ) ASN( A -81 ) THR( A -80 ) SER( A -79 ) ALA( A -78 ) SER( A -77 ) VAL( A -76 ) PRO( A -75 ) HIS( A -74 ) SER( A -73 ) MSE( A -72 ) ASP( A -71 ) GLU( A -70 ) SER( A -69 ) THR( A -68 ) ALA( A -67 ) LYS( A -66 ) GLY( A -65 ) ILE( A -64 ) LEU( A -63 ) LYS( A -62 ) TYR( A -61 ) LEU( A -60 ) HIS( A -59 ) ASP( A -58 ) LEU( A -57 ) GLY( A -56 ) VAL( A -55 ) PRO( A -54 ) VAL( A -53 ) SER( A -52 ) PRO( A -51 ) GLU( A -50 ) VAL( A -49 ) VAL( A -48 ) VAL( A -47 ) ALA( A -46 ) ARG( A -45 ) GLY( A -44 ) GLU( A -43 ) GLN( A -42 ) GLU( A -41 ) GLY( A -40 ) TRP( A -39 ) ASN( A -38 ) PRO( A -37 ) GLU( A -36 ) PHE( A -35 ) THR( A -34 ) LYS( A -33 ) LYS( A -32 ) VAL( A -31 ) ALA( A -30 ) GLY( A -29 ) TRP( A -28 ) ALA( A -27 ) GLU( A -26 ) LYS( A -25 ) VAL( A -24 ) ALA( A -23 ) SER( A -22 ) GLY( A -21 ) ASN( A -20 ) ARG( A -19 ) ILE( A -18 ) LEU( A -17 ) ILE( A -16 ) LYS( A -15 ) ASN( A -14 ) PRO( A -13 ) GLU( A -12 ) TYR( A -11 ) PHE( A -10 ) SER( A -9 ) THR( A -8 ) TYR( A -7 ) MSE( A -6 ) GLN( A -5 ) GLU( A -4 ) GLN( A -3 ) LEU( A -2 ) LYS( A -1 ) GLU( A 0 ) LEU( A 1 ) VAL( A 2 ) LEU( A 3 ) GLU( A 4 ) HIS( A 5 ) HIS( A 6 ) HIS( A 7 ) HIS( A 8 ) HIS( A 9 ) HIS( A 10 ) PDB Chain_ID: A 1 15 SEQRES: MSE VAL ASN PHE LYS ASP LYS SER MSE PRO THR ALA ILE GLU LYS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ALA LEU ASP PHE ILE GLY GLY MSE ASN THR SER ALA SER VAL PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: HIS SER MSE ASP GLU SER THR ALA LYS GLY ILE LEU LYS TYR LEU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: HIS ASP LEU GLY VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: GLY GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS VAL ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: GLY TRP ALA GLU LYS VAL ALA SER GLY ASN ARG ILE LEU ILE LYS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: ASN PRO GLU TYR PHE SER THR TYR MSE GLN GLU GLN LEU LYS GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: LEU VAL LEU GLU HIS HIS HIS HIS HIS HIS THR ALA ILE GLU LYS COORDS: ... ... ... ... ... ... ... ... ... ... THR ALA ILE GLU LYS 11 15 121 135 SEQRES: ALA LEU ASP PHE ILE GLY GLY MSE ASN THR SER ALA SER VAL PRO COORDS: ALA LEU ASP PHE ILE GLY GLY MSE ASN THR SER ALA SER VAL PRO 16 30 136 150 SEQRES: HIS SER MSE ASP GLU SER THR ALA LYS GLY ILE LEU LYS TYR LEU COORDS: HIS SER MSE ASP GLU SER THR ALA LYS GLY ILE LEU LYS TYR LEU 31 45 151 165 SEQRES: HIS ASP LEU GLY VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG COORDS: HIS ASP LEU GLY VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG 46 60 166 180 SEQRES: GLY GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS VAL ALA COORDS: GLY GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS VAL ALA 61 75 181 195 SEQRES: GLY TRP ALA GLU LYS VAL ALA SER GLY ASN ARG ILE LEU ILE LYS COORDS: GLY TRP ALA GLU LYS VAL ALA SER GLY ASN ARG ILE LEU ILE LYS 76 90 196 210 SEQRES: ASN PRO GLU TYR PHE SER THR TYR MSE GLN GLU GLN LEU LYS GLU COORDS: ASN PRO GLU TYR PHE SER THR TYR MSE GLN GLU GLN LEU LYS GLU 91 105 211 215 SEQRES: LEU VAL LEU GLU HIS COORDS: LEU VAL LEU GLU HIS 106 110