May. 10, 12:42:07 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 0.010 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. 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-101 ) ALA( A-100 ) GLY( A -99 ) GLN( A -98 ) SER( A -97 ) ASP( A -96 ) ARG( A -95 ) LYS( A -94 ) ALA( A -93 ) ALA( A -92 ) LEU( A -91 ) LEU( A -90 ) ASP( A -89 ) GLN( A -88 ) VAL( A -87 ) ALA( A -86 ) ARG( A -85 ) VAL( A -84 ) GLY( A -83 ) LYS( A -82 ) ALA( A -81 ) LEU( A -80 ) ALA( A -79 ) ASN( A -78 ) GLY( A -77 ) ARG( A -76 ) ARG( A -75 ) LEU( A -74 ) GLN( A -73 ) ILE( A -72 ) LEU( A -71 ) ASP( A -70 ) LEU( A -69 ) LEU( A -68 ) ALA( A -67 ) GLN( A -66 ) GLY( A -65 ) GLU( A -64 ) ARG( A -63 ) ALA( A -62 ) VAL( A -61 ) GLU( A -60 ) ALA( A -59 ) ILE( A -58 ) ALA( A -57 ) THR( A -56 ) ALA( A -55 ) THR( A -54 ) GLY( A -53 ) MSE( A -52 ) ASN( A -51 ) LEU( A -50 ) THR( A -49 ) THR( A -48 ) ALA( A -47 ) SER( A -46 ) ALA( A -45 ) ASN( A -44 ) LEU( A -43 ) GLN( A -42 ) ALA( A -41 ) LEU( A -40 ) LYS( A -39 ) SER( A -38 ) GLY( A -37 ) GLY( A -36 ) LEU( A -35 ) VAL( A -34 ) GLU( A -33 ) ALA( A -32 ) ARG( A -31 ) ARG( A -30 ) GLU( A -29 ) GLY( A -28 ) THR( A -27 ) ARG( A -26 ) GLN( A -25 ) TYR( A -24 ) TYR( A -23 ) ARG( A -22 ) ILE( A -21 ) ALA( A -20 ) GLY( A -19 ) GLU( A -18 ) ASP( A -17 ) VAL( A -16 ) ALA( A -15 ) ARG( A -14 ) LEU( A -13 ) PHE( A -12 ) ALA( A -11 ) LEU( A -10 ) VAL( A -9 ) GLN( A -8 ) VAL( A -7 ) VAL( A -6 ) ALA( A -5 ) ASP( A -4 ) GLU( A -3 ) HIS( A -2 ) LEU( A -1 ) GLU( A 0 ) HIS( A 1 ) HIS( A 2 ) HIS( A 3 ) HIS( A 4 ) HIS( A 5 ) HIS( A 6 ) PDB Chain_ID: A 1 15 SEQRES: MSE ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU ASP GLN VAL COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ALA ARG VAL GLY LYS ALA LEU ALA ASN GLY ARG ARG LEU GLN ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: LEU ASP LEU LEU ALA GLN GLY GLU ARG ALA VAL GLU ALA ILE ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: THR ALA THR GLY MSE ASN LEU THR THR ALA SER ALA ASN LEU GLN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: ALA LEU LYS SER GLY GLY LEU VAL GLU ALA ARG ARG GLU GLY THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: ARG GLN TYR TYR ARG ILE ALA GLY GLU ASP VAL ALA ARG LEU PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: ALA LEU VAL GLN VAL VAL ALA ASP GLU HIS LEU GLU HIS HIS HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: HIS HIS HIS ARG LYS ALA ALA LEU LEU ASP GLN VAL ALA ARG VAL COORDS: ... ... ... ARG LYS ALA ALA LEU LEU ASP GLN VAL ALA ARG VAL 7 18 121 135 SEQRES: GLY LYS ALA LEU ALA ASN GLY ARG ARG LEU GLN ILE LEU ASP LEU COORDS: GLY LYS ALA LEU ALA ASN GLY ARG ARG LEU GLN ILE LEU ASP LEU 19 33 136 150 SEQRES: LEU ALA GLN GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR COORDS: LEU ALA GLN GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR 34 48 151 165 SEQRES: GLY MSE ASN LEU THR THR ALA SER ALA ASN LEU GLN ALA LEU LYS COORDS: GLY MSE ASN LEU THR THR ALA SER ALA ASN LEU GLN ALA LEU LYS 49 63 166 180 SEQRES: SER GLY GLY LEU VAL GLU ALA ARG ARG GLU GLY THR ARG GLN TYR COORDS: SER GLY GLY LEU VAL GLU ALA ARG ARG GLU GLY THR ARG GLN TYR 64 78 181 195 SEQRES: TYR ARG ILE ALA GLY GLU ASP VAL ALA ARG LEU PHE ALA LEU VAL COORDS: TYR ARG ILE ALA GLY GLU ASP VAL ALA ARG LEU PHE ALA LEU VAL 79 93 196 201 SEQRES: GLN VAL VAL ALA ASP GLU COORDS: GLN VAL VAL ALA ASP GLU 94 99