May. 11, 04:04:46 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 1.3 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 -------------------------------------------------------------------------------- -9.9 ALA A 26 N - CA - C 101.3 111.2 -7.8 VAL A 32 N - CA - C 103.4 111.2 7.9 GLY A 45 N - CA - C 120.4 112.5 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 -85 ) ALA( A -84 ) LEU( A -83 ) THR( A -82 ) LEU( A -81 ) TYR( A -80 ) GLN( A -79 ) ARG( A -78 ) ASP( A -77 ) ASP( A -76 ) CYS( A -75 ) HIS( A -74 ) LEU( A -73 ) CYS( A -72 ) ASP( A -71 ) GLN( A -70 ) ALA( A -69 ) VAL( A -68 ) GLU( A -67 ) ALA( A -66 ) LEU( A -65 ) ALA( A -64 ) GLN( A -63 ) ALA( A -62 ) ARG( A -61 ) ALA( A -60 ) GLY( A -59 ) ALA( A -58 ) PHE( A -57 ) PHE( A -56 ) SER( A -55 ) VAL( A -54 ) PHE( A -53 ) ILE( A -52 ) ASP( A -51 ) ASP( A -50 ) ASP( A -49 ) ALA( A -48 ) ALA( A -47 ) LEU( A -46 ) GLU( A -45 ) SER( A -44 ) ALA( A -43 ) TYR( A -42 ) GLY( A -41 ) LEU( A -40 ) ARG( A -39 ) VAL( A -38 ) PRO( A -37 ) VAL( A -36 ) LEU( A -35 ) ARG( A -34 ) ASP( A -33 ) PRO( A -32 ) MSE( A -31 ) GLY( A -30 ) ARG( A -29 ) GLU( A -28 ) LEU( A -27 ) ASP( A -26 ) TRP( A -25 ) PRO( A -24 ) PHE( A -23 ) ASP( A -22 ) ALA( A -21 ) PRO( A -20 ) ARG( A -19 ) LEU( A -18 ) ARG( A -17 ) ALA( A -16 ) TRP( A -15 ) LEU( A -14 ) ASP( A -13 ) ALA( A -12 ) ALA( A -11 ) PRO( A -10 ) HIS( A -9 ) ALA( 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 ) HIS( A 1 ) PDB Chain_ID: A 1 15 SEQRES: MSE ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS LEU CYS ASP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: GLN ALA VAL GLU ALA LEU ALA GLN ALA ARG ALA GLY ALA PHE PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: SER VAL PHE ILE ASP ASP ASP ALA ALA LEU GLU SER ALA TYR GLY COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: LEU ARG VAL PRO VAL LEU ARG ASP PRO MSE GLY ARG GLU LEU ASP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: TRP PRO PHE ASP ALA PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: PRO HIS ALA LEU GLU HIS HIS HIS HIS HIS HIS HIS ALA LEU THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ALA LEU THR 2 4 91 105 SEQRES: LEU TYR GLN ARG ASP ASP CYS HIS LEU CYS ASP GLN ALA VAL GLU COORDS: LEU TYR GLN ARG ASP ASP CYS HIS LEU CYS ASP GLN ALA VAL GLU 5 19 106 120 SEQRES: ALA LEU ALA GLN ALA ARG ALA GLY ALA PHE PHE SER VAL PHE ILE COORDS: ALA LEU ALA GLN ALA ARG ALA GLY ALA PHE PHE SER VAL PHE ILE 20 34 121 135 SEQRES: ASP ASP ASP ALA ALA LEU GLU SER ALA TYR GLY LEU ARG VAL PRO COORDS: ASP ASP ASP ALA ALA LEU GLU SER ALA TYR GLY LEU ARG VAL PRO 35 49 136 150 SEQRES: VAL LEU ARG ASP PRO MSE GLY ARG GLU LEU ASP TRP PRO PHE ASP COORDS: VAL LEU ARG ASP PRO MSE GLY ARG GLU LEU ASP TRP PRO PHE ASP 50 64 151 162 SEQRES: ALA PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA PRO COORDS: ALA PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA PRO 65 76