May. 10, 22:27:27 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 1.0 degrees. All covalent bond angles lie within a 6.0*RMSD range about the standard dictionary values. 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 -72 ) ALA( A -71 ) ILE( A -70 ) GLN( A -69 ) SER( A -68 ) LYS( A -67 ) TYR( A -66 ) SER( A -65 ) ASN( A -64 ) THR( A -63 ) GLN( A -62 ) VAL( A -61 ) GLU( A -60 ) SER( A -59 ) LEU( A -58 ) ILE( A -57 ) ALA( A -56 ) GLU( A -55 ) ILE( A -54 ) LEU( A -53 ) VAL( A -52 ) VAL( A -51 ) LEU( A -50 ) GLU( A -49 ) LYS( A -48 ) HIS( A -47 ) LYS( A -46 ) ALA( A -45 ) PRO( A -44 ) THR( A -43 ) ASP( A -42 ) LEU( A -41 ) SER( A -40 ) LEU( A -39 ) MSE( A -38 ) ALA( A -37 ) LEU( A -36 ) GLY( A -35 ) ASN( A -34 ) CYS( A -33 ) VAL( A -32 ) THR( A -31 ) HIS( A -30 ) LEU( A -29 ) LEU( A -28 ) GLU( A -27 ) ARG( A -26 ) LYS( A -25 ) VAL( A -24 ) PRO( A -23 ) SER( A -22 ) GLU( A -21 ) SER( A -20 ) ARG( A -19 ) GLN( A -18 ) ALA( A -17 ) VAL( A -16 ) ALA( A -15 ) GLU( A -14 ) GLN( A -13 ) PHE( A -12 ) ALA( A -11 ) LYS( A -10 ) ALA( A -9 ) LEU( A -8 ) ALA( A -7 ) GLN( A -6 ) SER( A -5 ) VAL( A -4 ) LYS( A -3 ) SER( A -2 ) ASN( A -1 ) LEU( A 0 ) GLU( A 1 ) HIS( A 2 ) HIS( A 3 ) HIS( A 4 ) HIS( A 5 ) HIS( A 6 ) HIS( A 7 ) PDB Chain_ID: A 1 15 SEQRES: MSE ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL GLU SER LEU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ILE ALA GLU ILE LEU VAL VAL LEU GLU LYS HIS LYS ALA PRO THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: ASP LEU SER LEU MSE ALA LEU GLY ASN CYS VAL THR HIS LEU LEU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: GLU ARG LYS VAL PRO SER GLU SER ARG GLN ALA VAL ALA GLU GLN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: PHE ALA LYS ALA LEU ALA GLN SER VAL LYS SER ASN LEU GLU HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: HIS HIS HIS HIS HIS SER ASN THR GLN VAL GLU SER LEU ILE ALA COORDS: ... ... ... ... ... SER ASN THR GLN VAL GLU SER LEU ILE ALA 8 17 91 105 SEQRES: GLU ILE LEU VAL VAL LEU GLU LYS HIS LYS ALA PRO THR ASP LEU COORDS: GLU ILE LEU VAL VAL LEU GLU LYS HIS LYS ALA PRO THR ASP LEU 18 32 106 120 SEQRES: SER LEU MSE ALA LEU GLY ASN CYS VAL THR HIS LEU LEU GLU ARG COORDS: SER LEU MSE ALA LEU GLY ASN CYS VAL THR HIS LEU LEU GLU ARG 33 47 121 135 SEQRES: LYS VAL PRO SER GLU SER ARG GLN ALA VAL ALA GLU GLN PHE ALA COORDS: LYS VAL PRO SER GLU SER ARG GLN ALA VAL ALA GLU GLN PHE ALA 48 62 136 147 SEQRES: LYS ALA LEU ALA GLN SER VAL LYS SER ASN LEU GLU COORDS: LYS ALA LEU ALA GLN SER VAL LYS SER ASN LEU GLU 63 74 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS ASN( A 9) CG OD1 ND2 GLN( A 11) CG CD OE1 NE2 GLU( A 74) CG CD OE1 OE2