May. 11, 04:45:19 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 0.007 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 -------------------------------------------------------------------------------- 8.0 ASP A 36 N - CA - C 119.2 111.2 -7.0 PHE A 55 N - CA - C 104.2 111.2 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 -90 ) LYS( A -89 ) ILE( A -88 ) ILE( A -87 ) SER( A -86 ) ILE( A -85 ) SER( A -84 ) GLU( A -83 ) THR( A -82 ) PRO( A -81 ) ASN( A -80 ) HIS( A -79 ) ASN( A -78 ) THR( A -77 ) MSE( A -76 ) LYS( A -75 ) ILE( A -74 ) THR( A -73 ) LEU( A -72 ) SER( A -71 ) GLU( A -70 ) SER( A -69 ) ARG( A -68 ) GLU( A -67 ) GLY( A -66 ) MSE( A -65 ) THR( A -64 ) SER( A -63 ) ASP( A -62 ) THR( A -61 ) TYR( A -60 ) THR( A -59 ) LYS( A -58 ) VAL( A -57 ) ASP( A -56 ) ASP( A -55 ) SER( A -54 ) GLN( A -53 ) PRO( A -52 ) ALA( A -51 ) PHE( A -50 ) ILE( A -49 ) ASN( A -48 ) ASP( A -47 ) ILE( A -46 ) LEU( A -45 ) LYS( A -44 ) VAL( A -43 ) GLU( A -42 ) GLY( A -41 ) VAL( A -40 ) LYS( A -39 ) SER( A -38 ) ILE( A -37 ) PHE( A -36 ) HIS( A -35 ) VAL( A -34 ) MSE( A -33 ) ASP( A -32 ) PHE( A -31 ) ILE( A -30 ) SER( A -29 ) VAL( A -28 ) ASP( A -27 ) LYS( A -26 ) GLU( A -25 ) ASN( A -24 ) ASP( A -23 ) ALA( A -22 ) ASN( A -21 ) TRP( A -20 ) GLU( A -19 ) THR( A -18 ) VAL( A -17 ) LEU( A -16 ) PRO( A -15 ) LYS( A -14 ) VAL( A -13 ) GLU( A -12 ) ALA( A -11 ) VAL( A -10 ) PHE( A -9 ) GLU( 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: MSE LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS ASN THR MSE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: LYS ILE THR LEU SER GLU SER ARG GLU GLY MSE THR SER ASP THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: TYR THR LYS VAL ASP ASP SER GLN PRO ALA PHE ILE ASN ASP ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: LEU LYS VAL GLU GLY VAL LYS SER ILE PHE HIS VAL MSE ASP PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: ILE SER VAL ASP LYS GLU ASN ASP ALA ASN TRP GLU THR VAL LEU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: PRO LYS VAL GLU ALA VAL PHE GLU LEU GLU HIS HIS HIS HIS HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: HIS MET LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS ASN THR COORDS: ... MET LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS ASN THR 1 14 106 120 SEQRES: MET LYS ILE THR LEU SER GLU SER ARG GLU GLY MET THR SER ASP COORDS: MET LYS ILE THR LEU SER GLU SER ARG GLU GLY MET THR SER ASP 15 29 121 135 SEQRES: THR TYR THR LYS VAL ASP ASP SER GLN PRO ALA PHE ILE ASN ASP COORDS: THR TYR THR LYS VAL ASP ASP SER GLN PRO ALA PHE ILE ASN ASP 30 44 136 150 SEQRES: ILE LEU LYS VAL GLU GLY VAL LYS SER ILE PHE HIS VAL MET ASP COORDS: ILE LEU LYS VAL GLU GLY VAL LYS SER ILE PHE HIS VAL MET ASP 45 59 151 165 SEQRES: PHE ILE SER VAL ASP LYS GLU ASN ASP ALA ASN TRP GLU THR VAL COORDS: PHE ILE SER VAL ASP LYS GLU ASN ASP ALA ASN TRP GLU THR VAL 60 74 166 174 SEQRES: LEU PRO LYS VAL GLU ALA VAL PHE GLU COORDS: LEU PRO LYS VAL GLU ALA VAL PHE GLU 75 83 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS MET( A 1) SD MET( A 15) SD MET( A 26) SD MET( A 58) SD ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS MET( A 1) SE MET( A 15) SE MET( A 26) SE MET( A 58) SE ZR18_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 1) in Token 'MODRES' can not be found in coordinates ZR18_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 15) in Token 'MODRES' can not be found in coordinates ZR18_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 26) in Token 'MODRES' can not be found in coordinates ZR18_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 58) in Token 'MODRES' can not be found in coordinates